Mutant antibodies and conjugation thereof

ABSTRACT

The present invention relates to a polypeptide comprising 7 β-strands A, B, C, D, E, F, and G sequentially connected together by connecting chains of amino acids, and a first α-helix sequentially located on the EF chain between β-strands E and F, wherein the β-strands are arranged so as to form a first β-sheet comprising β-strands A, B, D, and E, and a second β-sheet comprising β-strands C, F and G, said first and second β-sheets being covalently bonded together so as to form a first Ig domain; wherein the EF chain between β-strands E and F comprises the sequence X 1 -X 2 -X 3 -X 4 -K 5 H 6  (SEQ ID NO:98), and X 1 , X 3  and X 4  are each independently any amino acid residue, characterized in that X 2  is selected from the group consisting of A, G, I, V, L, R, S, T, Q, P, N, M, H, W, and pharmaceutically acceptable salts, stereoisomers, tautomers, solvates, and prodrugs thereof

This application claims the benefit of U.S. Provisional Application No.61/584,675 filed on Jan. 9, 2012, the contents of which is herebyincorporated by reference in its entirety.

REFERENCE TO SEQUENCE LISTING

This application is being filed electronically via EFS-Web and includesan electronically submitted sequence listing in .txt format. The .txtfile contains a sequence listing entitled“PC71862ACorrectedSequenceListing.txt” created on Jan. 21, 2013 andhaving a size of 263 KB. The sequence listing contained in this .txtfile is part of the specification and is herein incorporated byreference in its entirety.

BACKGROUND

The development of bifunctional therapeutics has great potential toaugment combination therapy strategies. A bifunctional therapeutic canprovide the benefit of a combination therapy by modulating 2 differentpathways with one therapeutic entity. In addition, bifunctionaltherapeutics may also benefit from synergies between pathways anddemonstrate increased activity compared to mono-functional agents.Furthermore, bifunctional therapeutics can provide benefits in terms ofreduced manufacturing, storage, and shipping costs, as well as reducingthe number of therapies given to the patient and simplifying dosageregimes.

The reference to any art in this specification is not, and should not betaken as, an acknowledgement of any form or suggestion that thereferenced art forms part of the common general knowledge.

SUMMARY OF THE INVENTION

The present invention provides a polypeptide comprising an antibodyconstant domain, the antibody constant domain comprising residues K andH at positions corresponding to positions 80 and 81 of SEQ ID NO:6 whensaid antibody constant domain is aligned with the sequence of SEQ IDNO:6, and characterized in that the antibody constant domain furthercomprises a residue selected from the group consisting of A, G, I, V, L,R, S, T, Q, P, N, M, H, W at a position corresponding to position 77 ofSEQ ID NO:6.

In some aspects, the invention provides an antibody constant domaincomprising SEQ ID NO:98 (and all sequences herein described that fallwithin the scope of SEQ ID NO:98), wherein the position of SEQ ID NO:98on said constant domain corresponds to residues 76-81 of SEQ ID NO:6when the constant domain sequence is aligned with SEQ ID NO:6.

Sequences may be aligned by structural alignment, where the structure ofthe two polypeptides are known, or by sequence alignment; when sequencealignment is used, the method is preferably augmented using structuralknowledge of homologous polypeptides whose structures are known.

The present invention provides a polypeptide comprising an antibodyconstant light domain, the antibody constant domain comprising residuesK188 and H181 according to Kabat numbering, and characterized in thatthe antibody constant domain further comprises a residue selected fromthe group consisting of A, G, I, V, L, R, S, T, Q, P, N, M, H, W at aposition corresponding to position 185 according to Kabat numbering.

The present invention provides a polypeptide comprising animmunoglobulin domain comprising 7 β-strands A, B, C, D, E, F, and Gsequentially connected together by chains of connecting amino acids,wherein the β-strands are arranged so as to form a first β-sheetcomprising β-strands A, B, D, and E, and a second β-sheet comprisingβ-strands C, F and G, said first and second β-sheets being covalentlybonded together; wherein β-strands E and F are connected together by anEF chain, and said EF chain comprises the sequence, X¹-X²-X³-X⁴-K⁵⁻H⁶(SEQ ID NO:98), and wherein X¹, X³ and X⁴ are each independently anyamino acid residue, and characterized in that X² is selected from thegroup consisting of A, G, I, V, L, R, S, T, Q, P, N, M, H, W, andpharmaceutically acceptable salts, stereoisomers, tautomers, solvates,and prodrugs thereof.

X² may be selected from the group consisting of A, G, I, L, R, S, T, P,N, and M (SEQ ID NO:99). X² may be selected from the group consisting ofA, G, I, L, S, T, P, and M (SEQ ID NO:100). In some aspects, the EFchain comprises a sequence selected from the group consisting ofsequence SEQ ID NO:101, SEQ ID NO:102, and SEQ ID NO:103. X² may beselected from the group consisting of A, G, I, V, L, R, S, T, Q, N, P,and M (SEQ ID NO:123). X² may be selected from the group consisting ofA, G, I, V, L, R, S, T, P, and M (SEQ ID NO:124). X² may be selectedfrom the group consisting of A, G, I, V, L, S, T, and M (SEQ ID NO:125).X² may be selected from the group consisting of A, G, I, L, S, T, and M(SEQ ID NO:126). X² may be S or T. X² may be A or G. X² may be I or L.The selections of X² described herein may also be applied to antibodyconstant domains of the invention, wherein position X² corresponds withresidue 77 of SEQ ID NO:6, or residue 185 of a constant light domainaccording to Kabat numbering.

In some aspects, the EF chain comprises a sequence selected from thegroup consisting of SEQ ID NO:98, SEQ ID NO:99, SEQ ID NO:100, SEQ IDNO:101, SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:115, SEQ ID NO:116, SEQID NO:117, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:125, and SEQ IDNO:126, and may further be selected from the group consisting of SEQ IDNO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:173, SEQ ID NO:174, SEQID NO:175, SEQ ID NO:176, SEQ ID NO:177, SEQ ID NO:178, SEQ ID NO:179,SEQ ID NO:180, SEQ ID NO:181, SEQ ID NO:182, SEQ ID NO:183, SEQ IDNO:184, SEQ ID NO:185, SEQ ID NO:186, SEQ ID NO:187, SEQ ID NO:188, SEQID NO:189, SEQ ID NO:190, SEQ ID NO:191, SEQ ID NO:192, SEQ ID NO:193,SEQ ID NO:194, SEQ ID NO:195, SEQ ID NO:196, SEQ ID NO:197, SEQ IDNO:198, SEQ ID NO:199, SEQ ID NO:200, SEQ ID NO:201, SEQ ID NO:202, SEQID NO:203, SEQ ID NO:204, SEQ ID NO:205, SEQ ID NO:206, SEQ ID NO:207,SEQ ID NO:208, SEQ ID NO:209, SEQ ID NO:210, SEQ ID NO:211, SEQ IDNO:212, SEQ ID NO:213, SEQ ID NO:214, SEQ ID NO:215, SEQ ID NO:216, SEQID NO:217, SEQ ID NO:218, SEQ ID NO:219, SEQ ID NO:220, SEQ ID NO:221,SEQ ID NO:222, SEQ ID NO:223, and SEQ ID NO:224.

In some aspects, there may be a single residue difference when comparedagainst residues 75-79 of SEQ ID NO:10; or SEQ ID NO:6. In some aspects,there may be up to 2 differences when compared against residues 75-79 ofSEQ ID NO:10; or SEQ ID NO:6. In some aspects, there may be up to 2differences when compared against residues 75-79 of SEQ ID NO:10; or SEQID NO:6. In some aspects, there may be up to 4 differences when comparedagainst residues 75-79 of SEQ ID NO:10; or SEQ ID NO:6. In some aspects,there may be up two non-sequential differences when compared againstresidues 75-79 of SEQ ID NO:10; or SEQ ID NO:6. In some aspects, theremay be up to three non-sequential differences when compared againstresidues 75-79 of SEQ ID NO:10; or SEQ ID NO:6.

In some aspects, there may be a single residue difference when comparedagainst residues 76-79 of SEQ ID NO:10; or SEQ ID NO:6. In some aspects,there may be up to 2 differences when compared against residues 76-79 ofSEQ ID NO:10; or SEQ ID NO:6. In some aspects, there may be up to 3differences when compared against residues 76-79 of SEQ ID NO:10; or SEQID NO:6. In some aspects, there may be up to 4 differences when comparedagainst residues 76-79 of SEQ ID NO:10; or SEQ ID NO:6. In some aspects,there may be up two non-sequential differences when compared againstresidues 76-79 of SEQ ID NO:10; or SEQ ID NO:6.

The polypeptide may comprise an EF α-helix located on the EF chain. Insome aspects, one or more of residues X¹, X², X³ and X⁴ of SEQ ID NO:98comprise part of the EF α-helix. In some aspects, two or more ofresidues X¹, X², X³ and X⁴ of SEQ ID NO:98 comprise part of the EFα-helix. In some aspects, three or more of residues X¹, X², X³ and X⁴ ofSEQ ID NO:98 comprise part of the EF α-helix. In some aspects, allresidues X¹, X², X³ and X⁴ of SEQ ID NO:98 comprise part of the EFα-helix. In some aspects, residues K⁵ and H⁶ of SEQ ID NO:98 do not formpart of an α-helix. The selections of X¹, X², X³, X⁴, K⁵, and H⁶described herein may also be applied to antibody constant domains of theinvention, wherein positions X¹, X², X³, X⁴, K⁵, and H⁶ correspond withresidues 76, 77, 78, 79, 800 and 81 of SEQ ID NO:6, or positions 184,185, 186, 187, 188 and 189 of a constant light domain according to Kabatnumbering.

In some aspects, the EF chain comprises a sequence selected from thegroup consisting of SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:101, SEQ IDNO:102, SEQ ID NO:103, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:117, SEQID NO:118, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:125, SEQ ID NO:126,SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:173, SEQ IDNO:174, SEQ ID NO:175, SEQ ID NO:176, SEQ ID NO:177, SEQ ID NO:178, SEQID NO:179, SEQ ID NO:180, SEQ ID NO:181, SEQ ID NO:182, SEQ ID NO:183,SEQ ID NO:184, SEQ ID NO:185, SEQ ID NO:186, SEQ ID NO:187, SEQ IDNO:188, SEQ ID NO:189, SEQ ID NO:190, SEQ ID NO:191, SEQ ID NO:192, SEQID NO:193, SEQ ID NO:194, SEQ ID NO:195, SEQ ID NO:196, SEQ ID NO:197,SEQ ID NO:198, SEQ ID NO:199, SEQ ID NO:200, SEQ ID NO:201, SEQ IDNO:202, SEQ ID NO:203, SEQ ID NO:204, SEQ ID NO:205, SEQ ID NO:206, SEQID NO:207, SEQ ID NO:208, SEQ ID NO:209, SEQ ID NO:210, SEQ ID NO:211,SEQ ID NO:212, SEQ ID NO:213, SEQ ID NO:214, SEQ ID NO:215, SEQ IDNO:216, SEQ ID NO:217, SEQ ID NO:218, SEQ ID NO:219, SEQ ID NO:220, SEQID NO:221, SEQ ID NO:222, SEQ ID NO:223, and SEQ ID NO:224.

In some aspects of the invention, and with particular reference to allsequences in the application with variability at a residue correspondingto X¹, X¹ according to the above sequences may be selected from thegroup consisting of A, I, V, L, G, P, F, W, Y, S, T, C, M, N, Q, K, R,H, E, and D. In some aspects, X¹ may be selected from the groupconsisting of A, I, V, L, G, F, W, Y, S, T, C, M, N, Q, K, R, H, E, andD. In some aspects, X¹ may be selected from the group consisting of A,I, V, L, F, W, Y, S, T, C, M, N, Q, K, R, H, E, and D. In some aspects,X¹ may be selected from the group consisting of A, I, V, L, F, W, Y, S,T, M, N, Q, K, R, H, E, and D. In some aspects, X¹ may be selected fromthe group consisting of A, I, V, L, S, T, M, N, Q, K, R, H, E, and D. Insome aspects, X¹ may be selected from the group consisting of A, I, V,L, S, T, M, N, Q, R, H, E, and D. X¹ may be selected from the groupconsisting of A, I, V, L, S, T, M, N, Q, E, and D. X¹ may be selectedfrom the group consisting of A, I, V, L, S, T, M, N, Q, E, and D. Theselections of X¹ described herein may also be applied to antibodyconstant domains of the invention, wherein position X¹ corresponds withresidue 76 of SEQ ID NO:6, or residue 184 of a constant light domainaccording to Kabat numbering.

In some aspects of the invention, and with particular reference to allsequences in the application with variability at a residue correspondingto X³, X³ according to the above sequences may be selected from thegroup consisting of A, I, V, L, G, P, F, W, Y, S, T, C, M, N, Q, K, R,H, E, and D. X³ may be selected from the group consisting of A, I, V, L,G, F, W, Y, S, T, C, M, N, Q, K, R, H, E, and D. X³ may be selected fromthe group consisting of A, I, V, L, F, W, Y, S, T, C, M, N, Q, K, R, H,E, and D. X³ may be selected from the group consisting of A, I, V, L, F,W, Y, S, T, M, N, Q, K, R, H, E, and D. X³ may be selected from thegroup consisting of I, L, F, W, Y, S, T, M, N, Q, K, R, H, E, and D. X³may be selected from the group consisting of I, L, F, W, Y, M, N, Q, K,R, H, E, and D. X³ may be selected from the group consisting of I, L, F,W, Y, N, Q, E, and D. X³ may be selected from the group consisting of I,L, F, W, and Y. X³ may be selected from the group consisting of F, W,and Y. X³ may be selected from the group consisting of W and Y. Theselections of X³ described herein may also be applied to antibodyconstant domains of the invention, wherein position X³ corresponds withresidue 78 of SEQ ID NO:6, or residue 186 of a constant light domainaccording to Kabat numbering. In some aspects of the invention, and withparticular reference to all sequences in the application withvariability at a residue corresponding to X⁴, X⁴ according to the abovesequences may be selected from the group consisting of A, I, V, L, G, P,F, W, Y, S, T, C, M, N, Q, K, R, H, E, and D. X⁴ may be selected fromthe group consisting of A, I, V, L, G, P, F, W, Y, S, T, M, N, Q, K, R,H, E, and D. X⁴ may be selected from the group consisting of A, I, V, L,G, F, W, Y, S, T, M, N, Q, K, R, H, E, and D. X⁴ may be selected fromthe group consisting of A, I, V, L, F, W, Y, S, T, M, N, Q, K, R, H, E,and D. X⁴ may be selected from the group consisting of A, I, V, L, G, S,T, M, N, Q, K, R, H, E, and D. X⁴ may be selected from the groupconsisting of A, I, V, L, S, T, M, N, Q, K, R, H, E, and D. X⁴ may beselected from the group consisting of I, L, S, T, M, N, Q, K, R, E, andD. X⁴ may be selected from the group consisting of S, T, M, N, Q, K, R,E, and D. X⁴ may be selected from the group consisting of S, T, N, Q, K,R, E, and D. X⁴ may be selected from the group consisting of N, Q, K, R,E, and D. X⁴ may be selected from the group consisting of N, Q, K, R,and E. X⁴ may be selected from the group consisting of, Q, K, and E. Theselections of X⁴ described herein may also be applied to antibodyconstant domains of the invention, wherein position X⁴ corresponds withresidue 79 of SEQ ID NO:6, or residue 187 of a constant light domainaccording to Kabat numbering.

In some aspects, the EF chain is between 6 and 12 residues long. In someaspects, the EF chain is between 7 and 12 residues long. In someaspects, the EF chain is between 8 and 12 residues long. In someaspects, the EF chain is between 9 and 12 residues long. In someaspects, the EF chain is between 6 and 11 residues long. In someaspects, the EF chain is between 6 and 10 residues long. In someaspects, the EF chain is between 6 and 9 residues long. In some aspects,the EF chain is between 7 and 11 residues long. In some aspects, the EFchain is between 7 and 10 residues long. In some aspects, the EF chainis between 8 and 10 residues long.

The EF chain may comprise an α-helix (the EF α-helix). The first residueof the EF α-helix may be located within the first 3 residues of the EFchain. The first residue of the EF α-helix may be located within thefirst 2 residues of the EF chain. The first residue of the EF α-helixmay be located at residue of the EF chain. The EF α-helix may compriseat least residues X¹ and X² of SEQ ID NO:98 or one of the correspondingsequences herein that fall within the scope of SEQ ID NO:98. In someaspects, residues K⁵ and H⁶ corresponding to SEQ ID NO:98 are not withinthe α-helix. In some aspects, residues KH that correspond to positions80 and 81 of SEQ ID NO:6 are not within the α-helix. In some aspects ofthe invention relating to antibody constant domains, the residuecorresponding to position 77 of SEQ ID NO:6 falls within an α-helix.

In some aspects, the immunoglobulin domain of the invention, which maybe a CL domain, further comprises the residue D, E, Q or N on theconnecting chain between β-strands C and D; the CD chain. In someaspects, the CL domain further comprises the residue D, E, Q or N on theCD chain, the residue being positioned so as to allow its amino acidside chain interact with at least one of the side chains of K⁵ or H⁶ ofSEQ ID NO:98. In some aspects, the polypeptide comprises a D, E, Q, or Nresidue located at the position corresponding to position 43 of SEQ IDNO:10 or SEQ ID NO:6, in some aspects, according to a BLAST sequencealignment. In some aspects, the residue is D, E or N. In some aspects,the residue is D or E. In some aspects the residue is D or N.

In some aspects, the β-strands C and D are connected together by a CDchain, comprising a CD motif C¹-C²-C³-C⁴ (SEQ ID NO:255) wherein each ofC¹, C², C³ and C⁴ may be any amino acid, or further specified as setforth below. The CD motif may be selected from the group consisting ofSEQ ID NO:245, SEQ ID NO:246, SEQ ID NO:247, SEQ ID NO:248, SEQ IDNO:249, SEQ ID NO:250, SEQ ID NO:251, SEQ ID NO:252, and SEQ ID NO:253,said CD motif beginning at the first or second residue of said CD chain.In some aspects, the CD motif begins at the first residue of the CDchain. In some aspects, the CD motif begins at the second residue of theCD chain. Favourably, the CD motif may not form part of an α-helix.

In some aspects, the residue C¹ of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, F, Y, W, N, Q, D, and E.In some aspects, the residue C¹ of the CD motif may be selected from thegroup consisting of I, L, V, M, P, F, Y, and W. In some aspects, theresidue C¹ of the CD motif may be selected from the group consisting ofI, L, V, P, F, Y, and W. In some aspects, the residue C¹ of the CD motifmay be selected from the group consisting of I, L, V, P, F, and W. Insome aspects, the residue C¹ of the CD motif may be selected from thegroup consisting of I, L, V, F, and W. In some aspects, the residue C¹of the CD motif may be selected from the group consisting of I, L, andV. In some aspects, the residue C¹ of the CD motif may be selected fromthe group consisting of L and V. In some aspects, the residue C¹ of theCD motif may be V. The selections of C¹ of the CD motif described hereinmay also be applied to antibody constant domains of the invention,wherein position C¹ of the CD motif corresponds with residue 42 of SEQID NO:6, or residue 150 of a constant light domain according to Kabatnumbering.

In some aspects, the residue C² of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, F, Y, W, N, Q, D, and E.In some aspects, the residue C² of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, F, Y, W, N, Q, D, and E.In some aspects, the residue C² of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, N, Q, D, and E. In someaspects, the residue C² of the CD motif may be selected from the groupconsisting of A, I, L, V, M, P, S, T, N, Q, D, and E. In some aspects,the residue C² of the CD motif may be selected from the group consistingof M, P, S, T, N, Q, D, and E. In some aspects, the residue C² of the CDmotif may be selected from the group consisting of S, T, N, Q, D, and E.In some aspects, the residue C² of the CD motif may be selected from thegroup consisting of N, Q, D, and E. In some aspects, the residue C² ofthe CD motif may be D. The selections of C² of the CD motif describedherein may also be applied to antibody constant domains of theinvention, wherein position C² of the CD motif corresponds with residue43 of SEQ ID NO:6, or residue 151 of a constant light domain accordingto Kabat numbering.

In some aspects, the residue C³ of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, F, Y, W, N, Q, D, and E.In some aspects, the residue C³ of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, F, Y, W, N, Q, D, and E.In some aspects, the residue C³ of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, N, Q, D, and E. In someaspects, the residue C³ of the CD motif may be selected from the groupconsisting of A, I, L, V, M, P, S, T, N, Q, D, and E. In some aspects,the residue C³ of the CD motif may be selected from the group consistingof M, P, S, T, N, Q, D, and E. In some aspects, the residue C³ of the CDmotif may be selected from the group consisting of S, T, N, Q, D, and E.In some aspects, the residue C³ of the CD motif may be selected from thegroup consisting of N, Q, D, and E. In some aspects, the residue C³ ofthe CD motif may be N. The selections of C³ of the CD motif describedherein may also be applied to antibody constant domains of theinvention, wherein position C³ of the CD motif corresponds with residue44 of SEQ ID NO:6, or residue 152 of a constant light domain accordingto Kabat numbering.

In some aspects, the residue C⁴ of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, F, Y, W, N, Q, D, and E.In some aspects, the residue C⁴ of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, F, Y, W, N, Q, D, and E.In some aspects, the residue C⁴ of the CD motif may be selected from thegroup consisting of A, I, L, G, V, M, P, S, T, N, Q, D, E, K, R, and H.In some aspects, the residue C⁴ of the CD motif may be selected from thegroup consisting of A, I, L, V, G, M, P, S, T, N, Q, D, and E. In someaspects, the residue C⁴ of the CD motif may be selected from the groupconsisting of A, I, L, V, G, S, T, N, Q, D, and E. In some aspects, theresidue C⁴ of the CD motif may be selected from the group consisting ofA, V, Q, and S. In some aspects, the residue C⁴ of the CD motif may beselected from the group consisting of A and S. In some aspects, theresidue C⁴ of the CD motif may be A. The selections of C⁴ of the CDmotif described herein may also be applied to antibody constant domainsof the invention, wherein position C⁴ of the CD motif corresponds withresidue 45 of SEQ ID NO:6, or residue 153 of a constant light domainaccording to Kabat numbering.

In some aspects, the CD chain is between 6 and 12 residues long. In someaspects, the CD chain is between 7 and 12 residues long. In someaspects, the CD chain is between 8 and 12 residues long. In someaspects, the CD chain is between 9 and 12 residues long. In someaspects, the CD chain is between 6 and 11 residues long. In someaspects, the CD chain is between 6 and 10 residues long. In someaspects, the CD chain is between 6 and 9 residues long. In some aspects,the CD chain is between 7 and 11 residues long. In some aspects, the CDchain is between 7 and 10 residues long. In some aspects, the CD chainis between 8 and 10 residues long.

The immunoglobulin domain may be an antibody domain. The antibody domainmay be an antibody constant domain. The antibody constant domain may bea constant heavy (CH) domain or constant light (CL) domain. Antibody CHdomains may be selected from the group consisting of CHα1, CHα2, CHα3,CHδ1, CHδ2, CHδ3, CHε1, CHε2, CHε3, CHε4, CHγ1, CHγ2, CHγ3, CHμ1, CHμ2,CHμ3, and CHμ4.

In some aspects, the immunoglobulin domains of the invention aremammalian in origin (notwithstanding the method used to generate anyartificially mutated or otherwise engineered versions). The mammalianspecies may be human, mouse, rabbit, rat, rodent, pig, cow, sheep, goat,donkey, horse, camel, primate, monkey, dog, or cat. The immunoglobulindomains of the invention, and other proteins such as antibodies to whichthey comprise or attached may be humanized.

In some aspects, the invention comprises mutant immunoglobulin domains,wherein a mutant is defined as sequence that has been engineered oraltered to a sequence other than its natural canonical sequence, suchthat certain embodiments of polypeptides of the invention specificallyexcludes naturally occurring sequences that fall within the scope of thedefinition. In some aspects, therefore, the present invention relates topolypeptides of the invention comprising an EF chain that differs fromtheir naturally occurring corresponding sequence.

The antibody domains of the invention may specifically exclude one ormore natural IgA constant heavy domains (CHα1, CHα2, CHα3) from one ormore species selected from the group consisting of Bornean orangutan andPongo pygmaeus, and/or one or more natural IgM constant heavy domains(CHμ1, CHμ2, CHμ3, and CHμ4) from one or more species selected from thegroup consisting of mouse, rat, horse, Equus caballus , Heterocephalusglaber, bat, Eptesicus fuscus, and/or one or more natural IgE constantheavy domains (CHε1, CHε2, CHε3, and CHε4) from one or more speciesselected from the group consisting of human, chimp, monkey, Erythrocebuspatas, mouse, rat, bat, Cynopterus sphinx, sheep, Ovis aries, echidna,and Tachyglossus aculeatus.

In some aspects, one or more constant heavy domains selected from thegroup consisting of CHα1, CHα2, CHα3, CHδ1, CHδ2, CHδ3, CHε1, CHε2,CHε3, CHε4, CHγ1, CHγ2, CHγ3, CHμ1, CHμ2, CHμ3, and CHμ4 from one ormore of the species selected from the group consisting of human, mouse,rabbit, rat, rodent, pig, cow, sheep, goat, donkey, horse, camel,primate, monkey, dog, or cat are specifically excluded.

In some aspects, the invention provides an immunoglobulin domain, thatmay be a constant light chain (CL) domain, comprising 7 β-strands A, B,C, D, E, F, and G sequentially connected together by chains of aminoacids, wherein the β-strands are arranged so as to form a first β-sheetcomprising β-strands A, B, D, and E, and a second β-sheet comprisingβ-strands C, F and G, said first and second β-sheets being covalentlybonded together; wherein the chain between β-strands E and F comprisesthe sequence X¹-X²-X³-X⁴-K⁵-H⁶ (SEQ ID NO:98), and X¹, X³ and X⁴ areeach independently any amino acid residue, and characterized in that X²is selected from the group consisting of A, G, I, V, L, R, S, T, Q, P,N, M, H, and W, and pharmaceutically acceptable salts, stereoisomers,tautomers, solvates, and prodrugs thereof. The invention also providesfor pharmaceutical compositions and samples comprising CL domains of theinvention. In some aspects, an α-helix is sequentially located on theconnecting chain between β-strands E and F.

In part, aspects of the invention are based on the surprising discoverythat site directed conjugation to a reactive KH group located on the EFchain of an immunoglobulin domain, that may be a constant light chain(CL) domain, is improved by a mutation 3 amino acid residues upstreamthat eliminates the presence of an acidic residue such as D or E, andthat avoids introducing the aromatic residues F or Y, or other potentialconjugation sites such as K or C.

Grafting a sequence of the invention onto the EF chain can impartincreased specificity of conjugation on immunoglobulin domains, inparticular, CL domains. This can be useful when conjugating Linkersand/or Effector Moieties onto immunoglobulin domains, and CL domains ingeneral, and antibody and antigen-binding portions thereof inparticular. In some aspects, therefore, the invention relates to a novelclass of Multifunctional Antibody Conjugates (MACS), comprising anantibody, or antigen binding portion thereof, covalently conjugated toan Linker and/or Effector Moiety via a linker, characterized in that theantibody or antigen binding portion thereof comprises a polypeptide ofthe invention, and the linker is covalently bonded to the ε-amino groupof the side chain of K⁵ of SEQ ID NO:98.

In some aspects, the immunoglobulin domain of the invention, that may bea CL domain, is connected to a variable light chain (VL) domain.Together, these may comprise an antibody light chain.

In some aspects, the covalent bond between the first and second β-sheetsis a disulfide bond. In some aspects, the disulfide bond is betweenβ-strands B and F.

The CL domain may be a constant light chain kappa (CLκ), and may be ofrat, mouse, monkey, rabbit, goat, sheep, cow, pig, horse, donkey, dog,cat, or human origin. In some aspects, the CLκ comprises a sequenceselected from the group consisting of SEQ ID NO:37, SEQ ID NO:38, SEQ IDNO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:44, SEQ IDNO:46, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ IDNO:52, SEQ ID NO:54, SEQ ID NO:104, SEQ ID NO:105, SEQ ID NO:106, SEQ IDNO:119, SEQ ID NO:120, SEQ ID NO:121, and SEQ ID NO:122.

In some aspects, the CLκ comprises an N-terminal portion defined by SEQID NO:225 and a C′ terminal portion defined by SEQ ID NO:226contiguously connected together by an intermediate sequence selectedfrom the group consisting of SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:101,SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:115, SEQ ID NO:116, SEQ IDNO:117, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:125, SEQID NO:126, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:173,SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, SEQ ID NO:177, SEQ IDNO:178, SEQ ID NO:179, SEQ ID NO:180, SEQ ID NO:181, SEQ ID NO:182, SEQID NO:183, SEQ ID NO:184, SEQ ID NO:185, SEQ ID NO:186, SEQ ID NO:187,SEQ ID NO:188, SEQ ID NO:189, SEQ ID NO:190, SEQ ID NO:191, SEQ IDNO:192, SEQ ID NO:193, SEQ ID NO:194, SEQ ID NO:195, SEQ ID NO:196, SEQID NO:197, SEQ ID NO:198, SEQ ID NO:199, SEQ ID NO:200, SEQ ID NO:201,SEQ ID NO:202, SEQ ID NO:203, SEQ ID NO:204, SEQ ID NO:205, SEQ IDNO:206, SEQ ID NO:207, SEQ ID NO:208, SEQ ID NO:209, SEQ ID NO:210, SEQID NO:211, SEQ ID NO:212, SEQ ID NO:213, SEQ ID NO:214, SEQ ID NO:215,SEQ ID NO:216, SEQ ID NO:217, SEQ ID NO:218, SEQ ID NO:219, SEQ IDNO:220, SEQ ID NO:221, SEQ ID NO:222, SEQ ID NO:223, and SEQ ID NO:224.

The immunoglobulin domain may be a CLλ domain, and may comprise asequence selected from the group consisting of SEQ ID NO:60, SEQ IDNO:61, SEQ ID NO:141, SEQ ID NO:144, SEQ ID NO:143, SEQ ID NO:236, SEQID NO:237, SEQ ID NO:238, SEQ ID NO:239, SEQ ID NO:240, SEQ ID NO:241,SEQ ID NO:242, SEQ ID NO:243, and SEQ ID NO:244. In some aspects, theCLλ domain comprises a sequence selected from the group consisting ofSEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:143, SEQ ID NO:236, SEQ ID NO:237,SEQ ID NO:238, SEQ ID NO:239, SEQ ID NO:240, SEQ ID NO:241, SEQ IDNO:242, SEQ ID NO:243, and SEQ ID NO:244.

The CLλ may comprise an N′ terminal portion defined by one of SEQ IDNO:227, SEQ ID NO:228, SEQ ID NO:229, SEQ ID NO:230, SEQ ID NO:231, SEQID NO:232, or SEQ ID NO:233 contiguously connected together by anintermediate sequence to a C′ terminal portion defined by either of SEQID NO:234 or SEQ ID NO:235, the intermediate sequence being selectedfrom the group consisting of SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:101,SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:115, SEQ ID NO:116, SEQ IDNO:117, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:125, SEQID NO:126, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:173,SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, SEQ ID NO:177, SEQ IDNO:178, SEQ ID NO:179, SEQ ID NO:180, SEQ ID NO:181, SEQ ID NO:182, SEQID NO:183, SEQ ID NO:184, SEQ ID NO:185, SEQ ID NO:186, SEQ ID NO:187,SEQ ID NO:188, SEQ ID NO:189, SEQ ID NO:190, SEQ ID NO:191, SEQ IDNO:192, SEQ ID NO:193, SEQ ID NO:194, SEQ ID NO:195, SEQ ID NO:196, SEQID NO:197, SEQ ID NO:198, SEQ ID NO:199, SEQ ID NO:200, SEQ ID NO:201,SEQ ID NO:202, SEQ ID NO:203, SEQ ID NO:204, SEQ ID NO:205, SEQ IDNO:206, SEQ ID NO:207, SEQ ID NO:208, SEQ ID NO:209, SEQ ID NO:210, SEQID NO:211, SEQ ID NO:212, SEQ ID NO:213, SEQ ID NO:214, SEQ ID NO:215,SEQ ID NO:216, SEQ ID NO:217, SEQ ID NO:218, SEQ ID NO:219, SEQ IDNO:220, SEQ ID NO:221, SEQ ID NO:222, SEQ ID NO:223, and SEQ ID NO:224.

In some embodiments where the immunoglobulin domain comprises a CLλdomain, the domain may further comprise a CD motif as described herein.

In some embodiments where the immunoglobulin domain comprises a CHγ1domain, the domain may further comprise a CD motif as described herein.

In some embodiments where the immunoglobulin domain comprises a CHγ2domain, the domain may further comprise a CD motif as described herein.

In some embodiments where the immunoglobulin domain comprises a CHγ3domain, residue X² of the EF chain may not be R; in some aspects, the EFchain sequence may be selected from the group consisting of SEQ IDNO:100, SEQ ID NO:103, SEQ ID NO:117, SEQ ID NO:125, SEQ ID NO:203, SEQID NO:204, SEQ ID NO:205, SEQ ID NO:206, SEQ ID NO:207, SEQ ID NO:208,SEQ ID NO:209, SEQ ID NO:210, SEQ ID NO:211, SEQ ID NO:212, SEQ IDNO:213, SEQ ID NO:214, SEQ ID NO:215, SEQ ID NO:216, SEQ ID NO:217, SEQID NO:218, SEQ ID NO:219, SEQ ID NO:220, SEQ ID NO:221, SEQ ID NO:222,SEQ ID NO:223, and SEQ ID NO:224. IN some aspects, the CD chain of aCHγ3 domain of the invention may further comprise a CD motif asdescribed herein.

When conjugated to a linker suitable for conjugation to an EffectorMoiety, the ε-amino group of the side chain of K⁵ of SEQ ID NO:98 may becovalently attached to the linker.

In part, the invention is based on the surprising discovery thatmutating CLκ-D⁷⁷ to one of A, G, I, V, L, R, S, T, Q, P, N, M, H, or Wprovides a significant increase in the degree of specificity ofconjugation to CLκ-K⁸⁰.

Reaction of the Effector Moiety with the constant light domain of anantibody is particularly desirable to minimize, or prevent, anyinterference with binding of the Fc portion of the antibody to Fcreceptors (such as FcγR and FcRn) or binding of the antibody to itsrespective target. Conversely, conjugation of the respective EffectorMoiety to the Fc portion of an antibody may decrease the antibodyhalf-life in vivo and/or its capacity to interact with the immune system(effector function). Conjugation of the Effector Moiety in the variableheavy chain (VH) or variable light chain (VL) region of the antibodycarry a risk of diminishing the binding of the antibody to its cognate.

Preferential conjugation of the Effector Moiety to the CLκ or theconstant light chain lambda (CLλ) domain simplifies the creation of MACisotypes by allowing isotypic switches of the constant heavy chain (CH)domains of the antibody without affecting the conjugation sites of theEffector Moiety to the antibody.

The Linker and/or Effector Moiety may be covalently attached to the sidechain of CLκ-K⁸⁰ (for example, a sequence selected from the groupconsisting of SEQ ID NO:104, SEQ ID NO:105, SEQ ID NO:106, SEQ IDNO:119, SEQ ID NO:120, SEQ ID NO:121, and SEQ ID NO:122.). The CL islocated away from key regions of a typical antibody upon which it wouldform a part of, such as paratope region, FcRn binding domain, hinge, FcRbinding domains; this provides the advantage that preferentially linkingat these sites limits the amount of interference to antibody-antigeninteraction when the MAC is conjugated to the Effector Moiety.

In some aspect, the CLκ region comprises at least residues 62-103 of SEQID NO:104, SEQ ID NO:105, SEQ ID NO:106, SEQ ID NO:107, SEQ ID NO:108,or SEQ ID NO:109, SEQ ID NO:119, SEQ ID NO:120, SEQ ID NO:121, or SEQ IDNO:122. In some aspects, CLκ-x⁸² may be any amino acid. In some aspects,CLκ-x⁸² may be selected from the group consisting of K, R, G, A, V, L,I, S, T, C, M, N, Q, D, E, H, F, W and Y. In some aspects, CLκ-x⁸² maybe G, A, V, L, or I. In some aspects, CLκ-x⁸² may be K, R, N, or Q. Insome aspects, CLκ-x⁸² may be D, or E. In some aspects, CLκ-x⁸² may be K,R, G, A, V, L, I, N, or Q. In some aspects, CLκ-x⁸² may be D, or E. Insome aspects, CLκ-x⁸² may be K, R, G, A, V, L, I, N, Q, D or E. In someaspects, CLκ-x⁸² may be D, or E. In some aspects, CLκ-x⁸² may be H, F, Wor Y. In some aspects CLκ-x⁸² is not proline. In some aspects, CLκ-x⁸²is K. In some aspects, CLκ-x⁸² is R.

In some aspects, antibodies of the invention, or antigen-bindingportions thereof, comprise an Effector Moiety conjugated to K⁵ of SEQ IDNO:98 on both light chains. In some aspects, the Effector Moiety isconjugated to K⁵ of SEQ ID NO:98 on one light chain only. In someaspects, the Effector Moiety is only conjugated to K⁵ of SEQ ID NO:98.In some aspects, the Effector Moiety is conjugated at K⁵ of SEQ ID NO:98on one light chain and one other location on the antibody, orantigen-binding portions thereof. In some aspects, the Effector Moietyis conjugated at K⁵ of SEQ ID NO:98 on one light chain and 2 otherlocations on the antibody, or antigen-binding portions thereof. In someaspects, the Effector Moiety is conjugated to K⁵ of SEQ ID NO:98 on onelight chain and 3 other locations on the antibody, or antigen-bindingportions thereof. In some aspects, the Effector Moiety is conjugated toK⁵ of SEQ ID NO:98 on both light chains, and at one other location. Insome aspects, the Effector Moiety is conjugated at K⁵ of SEQ ID NO:98 onboth light chains, and at 2 other locations. In some aspects, theEffector Moiety is conjugated at K⁵ of SEQ ID NO:98 on both lightchains, and at 3 other locations.

In some aspects, the invention relates to a mutated Immunoglobulin (Ig)domain, comprising a substituted residue within the mutated Ig domainthat corresponds to position 77 of SEQ ID NO:10; or SEQ ID NO:6,characterized in that the substituted residue is selected from the groupconsisting of A, G, I, V, L, R, S, T, M, Q, N, P, H, and W, providedthat the mutated Ig domain further comprises residues K and H atpositions corresponding to positions 80 and 81 respectively of SEQ IDNO:10; or SEQ ID NO:6. In some aspects, the mutated Ig domain comprisesa sequence selected from the group consisting of SEQ ID NOs: 38, 39, 40,41, 42, 44, 46, 47, 49, 50, 51, 52, 54, 98, 99, 100, 101, 102, 103, 104,105, 106, 107, 108, 109, 115, 116, 117, 119, 120, 121, 122, 123, 124,125, and 126.

Deposits

In some aspects, the invention provides for vectors and nucleic acids asdeposited with the ATCC, polypeptides encoded by said vectors andnucleic acids, compositions comprising polypeptides encoded by saidvectors and nucleic acids, and polypeptides expressed by said nucleicacids and vectors. The following materials have been deposited with theAmerican Type Culture Collection, 10801 University Boulevard, Manassas,Va. 20110-2209, USA (ATCC):

Material SEQ ID NO: ATCC Accession No. Date of Deposit hCLk-Km(3)-D77A 37 PTA-13394 Dec. 12, 2012 h38C2-[LC-D185A] 254 PTA-13395 Dec. 12, 2012

Vector hCLk-Km(3)-D77A is a TA cloning vector with a polynucleotide DNAinsert encoding the human constant light chain kappa (Km(3)) domain witha D77A mutation, as set forth in SEQ ID NO:37, and vectorh38C2-[LC-D185A] is a polynucleotide DNA insert encoding the humanized38C2 light chain with a D77A mutation, as set forth in SEQ ID NO:254.

In some aspects, the invention provides for an isolated host cell thatrecombinantly produces an immunoglobulin domain of the presentinvention, or immunoglobulin domain-comprising protein or antibody ofthe present invention. The present invention provides for an isolatedpolynucleotide comprising a nucleotide sequence encoding proteins,domains and antibodies of the present invention, and vectors comprisingsaid polynucleotides. Vectors of the present invention may comprise ATCCdeposit sequences. In some aspects, the invention provides for a methodof producing an antibody, immunoglobulin domain, or protein, comprisingculturing a host cell under conditions that result in production of theantibody, immunoglobulin domain, or protein, and isolating the antibody,immunoglobulin domain, or protein, from the host cell or culture.

In some aspects, the present invention provide a polypeptide comprisinga sequence selected from the group consisting of SEQ ID NO:37, SEQ IDNO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ IDNO:44, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:50, SEQ IDNO:51, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:60, SEQ ID NO:61, SEQ IDNO:77, SEQ ID NO:78, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ IDNO:97, SEQ ID NO:104, SEQ ID NO:105, SEQ ID NO:106, SEQ ID NO:119, SEQID NO:120, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:127, SEQ ID NO:128,SEQ ID NO:129, SEQ ID NO:134, SEQ ID NO:135, SEQ ID NO:140, SEQ IDNO:141, SEQ ID NO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:148, SEQID NO:149, SEQ ID NO:150, SEQ ID NO:151, SEQ ID NO:156, SEQ ID NO:158,SEQ ID NO:159, SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:163, SEQ IDNO:165, SEQ ID NO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:236, SEQID NO:237, SEQ ID NO:238, SEQ ID NO:239, SEQ ID NO:240, SEQ ID NO:241,and SEQ ID NO:254, or a polypeptide that is at least about 85%, or atleast about 90%, or at least about 95%, or at least about 96%, or atleast about 97%, or at least about 98%, or at least about 99% identicalto one or more of the aforementioned sequences.

Samples and Compositions of the Invention

In some aspects, the invention provides for a composition or sample ofan antibody or antigen binding portion thereof comprising a CL domain ofthe invention covalently conjugated to an Effector Moiety, wherein atleast about 50% of the Effector Moiety in the composition or sample isconjugated to K⁵ of SEQ ID NO:98. In some aspects, it is at least about60%. In some aspects, it is at least about 70%. In some aspects, it isat least about 80%. In some aspects, it is at least about 90%.

In some aspects, the invention provides for a composition (or sample) ofa antibody or antigen binding portion thereof comprising a CL domain ofthe invention, wherein at least about 50% of the antibody comprises anEffector Moiety covalently attached to K⁵ of SEQ ID NO:98 on at leastone light chain. In some aspects, it is at least about 60%. In someaspects, it is at least about 70%. In some aspects, it is at least about80%. In some aspects, it is at least about 90%. In some aspects, theEffector Moiety is covalently conjugated to K⁵ of SEQ ID NO:98 on bothlight chain constant regions.

In some aspects, the invention provides for a composition (or sample) ofa antibody or antigen binding portion thereof comprising a CL domain ofthe invention covalently conjugated to an Effector Moiety, wherein atleast about 30% of the sample comprises Effector Moieties conjugated atabout 2 locations per antibody, and wherein at least one Effector Moietyconjugation site is K⁵ of SEQ ID NO:98. In some aspects, the amount isabout 40%. In some aspects, the amount is about 50%. In some aspects,the amount is about 60%. In some aspects, the amount is about 70%. Insome aspects, the amount is about 80%. In some aspects, the amount isabout 90%. In some aspects, the amount is about 95%. In some aspects,the amount is about 99%.

In some aspects, the invention provides for a composition (or sample) ofa antibody or antigen binding portion thereof comprising a CL domain ofthe invention covalently conjugated to an Effector Moiety, wherein atleast about 30% of the sample comprises Effector Moieties conjugated atabout 3 locations per antibody, and wherein at least 2 Effector Moietyconjugation sites are K⁵ of SEQ ID NO:98 on each light chain. In someaspects, the amount is about 40%. In some aspects, the amount is about50%. In some aspects, the amount is about 60%. In some aspects, theamount is about 70%. In some aspects, the amount is about 80%. In someaspects, the amount is about 90%. In some aspects, the amount is about95%. In some aspects, the amount is about 99%.

In some aspects, the invention provides for a composition (or sample) ofa antibody or antigen binding portion thereof comprising a CL domain ofthe invention, wherein at least 50% of the light chain molecules areconjugated with at least one Effector Moiety at K⁵ of SEQ ID NO:98. Insome aspects, it is at least about 60%. In some aspects, it is at leastabout 65%. In some aspects, it is at least about 70%. In some aspects,it is at least about 75%. In some aspects, it is at least about 80%. Insome aspects, it is at least about 85%. In some aspects, it is at leastabout 90%. In some aspects, it is at least about 95%.

In some aspects, the invention provides for a composition (or sample) ofa antibody or antigen binding portion thereof comprising a CL domain ofthe invention conjugated to an Effector Moiety at K⁵ of SEQ ID NO:98,wherein at least about 70% of the heavy chain molecules are unconjugatedwith the Effector Moiety. In some aspects, the amount is about 75%. Insome aspects, the amount is about 80%. In some aspects, the amount isabout 85%. In some aspects, the amount is about 90%. In some aspects,the amount is about 95%. In some aspects, the amount is about 99%. Insome aspects, substantially all of the heavy chain molecules areunconjugated with the Effector Moiety.

In some aspects, the amount of individual light chain fragments that areunconjugated has a lower limit selected from the group consisting ofabout 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, and 55%, and an upperlimit selected from the group consisting of about 5, 10, 15, 20, 25, 30,35, 40, 45, 50, 55, and 60%. In some aspects, the amount of individuallight chain fragments that are conjugated at one location has a lowerlimit selected from the group consisting of about 25, 30, 35, 40, 45,50, and 55%, and an upper limit selected from the group consisting ofabout 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, and 95%. Insome aspects, the amount of individual light chain fragments that areconjugated at 2 locations has a lower limit selected from the groupconsisting of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 5, 10, 15, 20, and 25%,and an upper limit selected from the group consisting of about 5, 16, 7,8, 9, 5, 10, 15, 20, 25, 30, 35, and 40%.

In some aspects, the amount of individual heavy chain fragments that areunconjugated has a lower limit selected from the group consisting ofabout 50, 55, 60, 65, 70, 75, and 80% and an upper limit selected fromthe group consisting of about 60, 65, 70, 75, 80, 85, 90, 95, and 99%.In some aspects, the amount of individual heavy chain fragments that areconjugated at one location has a lower limit selected from the groupconsisting of about 1, 2, 5, 10, 15, 20, and 25% and an upper limitselected from the group consisting of about 5, 10, 15, 20, 25, 30, 35,40, and 50%. In some aspects, the amount of individual heavy chainfragments that are conjugated at 2 locations has a lower limit selectedfrom the group consisting of about 0, 1, 2, 3, 4, 5, 10, and 15% and anupper limit selected from the group consisting of about 2, 3, 4, 5, 10,15 and 20%.

In some aspects the number of conjugations per antibody in a sample orcomposition of the invention has a lower limit selected from the groupconsisting of about 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5,1.55, 1.6, 1.65, 1.7, 1.75, 1.8, 1.85, 1.9, 1.95 and 2, and an upperlimit selected from the group consisting of about 1.6, 1.7, 1.75 1.8,1.85, 1.9, 1.95, 2.0, 2.05, 2.1, 2.15, 2.2, 2.25, 2.3, 2.4, 2.5, 2.6,2.7, 2.8, 2.9, 3.0, 3.5, 4.0, 4.5 and 5. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 1.5 and about 2.5. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 1.6 and about 2.4. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 1.7 and about 2.3. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 1.8 and about 2.2. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isan amount selected from the group consisting of about 1.5, about 1.55,about 1.6, about 1.65, about 1.7, about 1.75, about 1.8, about 1.85,about 1.9, about 1.95, about 2.0, about 2.05, about 2.1, about 2.15,about 2.2, about 2.25, about 2.3, about 2.4 and about 2.5. In someaspects, the amount is about 1.7. In some aspects, the amount is about1.8. In some aspects, the amount is about 1.9. In some aspects, theamount is about 2. In some aspects, the amount is about 2.1. In someaspects, the amount is about 2.1. In some aspects, the amount is about2.3.

In some aspects of the invention, the number of conjugations perantibody is less than 2, with at least 50% of the antibody populationhaving only a single conjugation per antibody. These samples areadvantageous as they allow additional conjugation reactions to betargeted at the remaining CLκ site. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 0.5 and about 1.5. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 0.6 and about 1.4. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 0.7 and about 1.3. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 0.8 and about 1.2. In some aspects the number ofconjugations per antibody in a sample or composition of the invention isbetween about 0.9 and about 1.1.

One of the advantages of the invention is that depending on the reagentsand reaction conditions (especially the leaving group ester and molarratio of linker:antibody), compositions and samples of the invention canbe generated with a defined number of Effector Moieties relative to adefined number of antibodies. This can be especially useful whenbalancing the relative reactivities and therapeutic windows of theEffector Moiety and antibody. Moreover, in some situations, increasingthe number of peptides or other Active Moieties per antibody beyond acertain threshold may not result in increased target binding ortherapeutic effect. It is useful, therefore, to be able to control thenumber of peptides conjugated per antibody, and in doing so, direct thelocation of conjugation so as to minimize Fc or combining siteinterference. In some situations, therefore, aspects of the inventionthat allow for reduced conjugation, preferentially decorating only asingle CLκ-K⁸⁰ can be advantageous. Furthermore, whereas conjugation toCLκ-K⁸⁰ is reliable and robust, conjugation to other antibody surfacelysines, each of slightly different reactivity and pI can result in anheterogeneous sample of conjugated antibodies that can releaseconjugated molecules at inopportune or irregular times, such as duringcirculation and prior to delivery of the Effector Moiety to the targetby antibody recognition (or delivery of the antibody to the target, byrecognition with the Effector Moiety). This can be particularlyundesirable with toxins (i.e. a cytotoxic agent with potential utilityin killing tumors and tumor cells).

In some aspects, the toxin is an auristatin; a derivative of the naturalproduct dolastatin 10 (MMAD). Representative auristatins include MMAE(N-methylvaline-valine-dolaisoleuine-dolaproline-norephedrine) and MMAF(N-methylvaline-valine-dolaisoleuine-dolaproline-phenylalanine).

In some aspects, the antibody targets a different target within the samepathway as the Effector Moiety. In some aspects, the antibody targets adifferent target to the Effector Moiety.

In some aspects, the VH and VL of antibody used for conjugation may beuseful in the field of oncology. Suitable antibodies include; Rituximab,(Rituxan™), a chimeric, IgG1κ, anti-CD20 antibody, used to treat cancerand in particular non Hodgkin's lymphoma and also rheumatoid arthritis;Cetuximab (Erbitux™) a chimeric, IgG1κ, anti-EGF receptor antibody, usedto treat cancer, and in particular colon, head & neck cancer.

In some aspects, the antibody used for conjugation may be useful in thefield of auto-immune and other immunological disorders. Suitableantibodies include Infliximab (Remicade™) a chimeric, IgG1κ, anti-TNFαantibody, used to treat rheumatoid arthritis, ulcerative colitis,Crohn's disease, psoriasis, psoriatic arthritis, and ankylosingspondylitis; Adalimumab (Humira™) a human, IgG1κ, anti-TNFα antibody,used to treat rheumatoid arthritis, Crohn's disease, psoriasis,psoriatic arthritis, juvenile idiopathic arthritis and ankylosingspondylitis; Natalizumab (Tysabri™) a humanized, IgG4κ, anti-α4-integrinantibody used to treat multiple sclerosis, rheumatoid arthritis,psoriasis, juvenile idiopathic arthritis, psoriatic arthritis,ankylosing spondylitis, Crohn's disease; Omalizumab (Xolair™) ahumanized, IgG1κ, anti-IgE antibody used to treat allergic asthma;Ranibizumab (Lucentis™) a humanized, IgG1κ, anti-VEGF antibody, used totreat wet AMD; and Palivizumab (Synagis™) a humanized, IgG1κ, anti-RSVantibody, used to treat infective diseases, including respiratorysyncytical virus.

In some aspect, compounds and compositions of the invention may be usedto treat the above mentioned conditions.

Effector Moieties

The Effector Moiety may be a therapeutic agent, protein, peptide,nucleic acid, aptamer, small molecule, protein agonist, proteinantagonist, metabolic regulator, hormone, toxin, growth factor or otherregulatory protein, or may be a diagnostic agent, such as an enzyme thatmay be easily detected or visualized, such as horseradish peroxidase.

In some aspects, the Effector Moiety may be a protein or peptide, andmay be connected to the linker through a peptide-linking residue. Theprotein or peptide may comprise one or both of an amino-terminal cappinggroup R¹ and a carboxyl-terminal capping group R². R¹ may be CH₃,C(O)CH₃, C(O)CH₃, C(O)CH₂CH₃, C(O)CH₂CH₂CH₃, C(O)CH(CH₃)CH₃,C(O)CH₂CH₂CH₂CH₃, C(O)CH(CH₃)CH₂CH₃, C(O)C₆H₅, C(O)CH₂CH₂(CH₂CH₂O)₁₋₅Me,dichlorobenzoyl (DCB), difluorobenzoyl (DFB), pyridinyl carboxlate (PyC)or amido-2-PEG, an amino protecting group, a lipid fatty acid group or acarbohydrate. R² may be OH, NH₂, NH(CH₃), NHCH₂CH₃, NHCH₂CH₂CH₃,NHCH(CH₃)CH₃, NHCH₂CH₂CH₂CH₃, NHCH(CH₃)CH₂CH₃, NHC₆H₅, NHCH₂CH₂OCH₃,NHOCH₃, NHOCH₂CH₃, a carboxy protecting group, a lipid fatty acid groupor a carbohydrate.

The protein or peptide linking residue may be K, K_(SH), lysinehomologs, Dap, Dab, Orn, R, C, thiol containing residues, S, T, Y, D, E,N or Q. The protein or peptide may be connected to the linker throughthe amino terminus of the N-terminal amino acid. The protein or peptidemay be connected to the linker through the carboxyl terminus of theC-terminal amino acid. An additional amino acid residue may be added tothe N- or C-terminus in order to function as a linking residue, whetherby connection through the amino acid side chain, or the amino orcarboxyl terminus.

Linkers

In aspects of the invention relating to conjugates with EffectorMoieties, in particular methods of preparing conjugates and MACs, itwill be understood that the invention equally applies to conjugates withLinkers in the absence of Effector Moieties. An example of the utilityof such conjugates would be as intermediates that may usefully used toprepate Effector Moiety-linker-polypeptide conjugates of the invention.

The Effector Moiety of the invention (such as a small molecule, aptamer,nucleic acid, protein, or peptide) may be covalently attached to theantibody or antigen binding portion thereof by a linker. The linker maybe covalently attached to the peptide by an amino group of the sidechain of the peptide-linking residue. This may be a lysine residue. Insome embodiments, the linking residue is a thiol bearing residue, suchas Cys or K_(SH) and the linker is covalently attached to the peptidevia the terminal thiol group of the linking residue.

The linker may be linear or branched (to allow for conjugation to morethan one Effector Moiety per Conjugation Addition (CA)), and optionallyincludes one or more carbocyclic or heterocyclic groups. Linker lengthmay be viewed in terms of the number of linear atoms between theEffector Moiety and Antibody, with cyclic moieties such as aromaticrings and the like to be counted by taking the shortest route around thering. In some embodiments, the linker has a linear stretch of between5-15 atoms, in other embodiments 15-30 atoms, in still other embodiments30-50 atoms, in still other embodiments 50-100 atoms, and in still otherembodiments 100-200 atoms. In some embodiments, the length of the linkeris a range with a lower limit selected from the group consisting of 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130,140, 150, 160, 170, 180, 190, and an upper limit selected from the groupconsisting of 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25,30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110,120, 130, 140, 150, 160, 170, 180, 190, and 200.

Other linker considerations include the effect on physical orpharmacokinetic properties of the resulting compound, such assolubility, lipophilicity, hydrophilicity, hydrophobicity, stability(more or less stable as well as planned degradation), rigidity,flexibility, immunogenicity, modulation of antibody binding, the abilityto be incorporated into a micelle or liposome, and the like.

The linker may be a peptidyl linker. In some embodiments, the peptidyllinker may be between 3-20 amino acids long, such as repeats of a singleamino acid residue (e.g. polyglycine) or combinations of amino acidresidues to give a peptide linker which imparts favorable presentationof the Effector Moiety or pharmacokinetics. Peptidyl linkers that wouldbe most compatible with the presence of activating groups may lacklysine and histidine residues. SEQ ID NO:79 is an exemplary peptidyllinker.

Alternatively, the linker may be a non-peptidyl linker. Typical examplesof these types of linker would be those based on straight or branchedchain hydrocarbons or polyethylene glycols of varying lengths. These mayincorporate other groups to affect solubility, rigidity, isoelectricpoint, such as aromatic or non-aromatic rings, halogens, ketones,aldehydes, esters, sulfonyls, phosphate groups, and so on.

In some aspects of the invention, the linker may comprise the formula:—X¹—Y¹—Z—; wherein X¹ is the attachment group to the Effector Moiety(for example, via a peptide-linking residue), Y¹ is a spacer region, andZ is an attachment moiety to the side chain of a lysine residue on anantibody (for example, an anti-IGF1R antibody). In some aspects, thelinker may be of the formula X¹Y¹Z* when unbound to the antibody, whereZ* is a leaving group, such that when conjugated to the antibody, theleaving group Z* reacts with the conjugation site of the antibody toform the conjugated linker X¹Y¹Z.

X¹ may be selected so as to enable a specific directional covalentlinking strategy to the Effector Moiety (for example, via thepeptide-linking residue). In some aspects, X¹ may be selected from thegroup consisting of COOH, isocyanate, isothiocyanate, acyl azide,sulfonic acid, sulfonyl halide, aldehyde, ketone, epoxide, carbonate,arylating reagent, imidoester, amine group, and a malemide group. Forexample, where the peptide-linking residue comprises a nucleophilicgroup, X¹ may be an electrophilic group and vice versa. For example, ifthe peptide-linking residue side chain comprises an amine group, such asK, H, Ornithine, Dap, or Dab, X¹ may be COOH, or other similarlyreactive electrophile, for example, an isocyanate, isothiocyanate, acylazide, sulfonic acid or sulfonyl halide, aldehyde or ketone, epoxide,carbonate, arylating reagent or imidoester. If the peptide-linkingresidue is D or E, X¹ may comprise a nucleophilic group, such as anamine group. Either of these strategies permits a covalent bond to beformed between the X¹ group and the peptide-linking residue by amidebond formation strategies. For example, when X¹ is COOH, it may beactivated as a pentafluorophenyl ester. In this case, reaction with anamine group on the peptide-linking peptide leads to amide bondformation, while the pentafluorophenol is a leaving group (which may betermed X¹*).

The arrow indicates the point of attachment to the peptide-linkingresidue and the parallel line represents the point of attachment to theY¹ group of the linker.

Where the peptide-linking group is C, homologs of C, or otherthiol-group containing residues (such as K_(SH)), X¹ may comprise amalemide group, permitting a thiol-malemide addition reaction strategyto covalently link the X¹ group to the peptide-linking residue. In someaspects, X¹ may be maleimide:

wherein the arrow indicates the point of attachment to the peptidelinking residue and the parallel line represents to attachment to the Y¹group of the linker. For ease of nomenclature, linkers described hereinthat have been constructed using maleimide groups are described asmaleimide-containing linkers, and may be titled MAL to indicate this,even though following construction of the linker, the maleimide group isgenerally converted to a succinimide ring.

In some aspects, the linking residue is K_(SH), and the X¹ group ismaleimide. In some aspects, X¹ may comprise a pentafluorophenyl esteractivated carboxyl function which may form an amide with the lysine sidechain on the peptide.

In some aspects, X¹ may comprise a thiol group, allowing a disulphidebridge to be formed between the peptide-linking residue and X¹ group.

In some embodiments, Y¹ is a biologically compatible connecting chainincluding any atom selected from the group consisting of C, H, N, O, P,S, F, Cl, Br, and I, and may comprise one or more amino acids, polymeror block co-polymer. Y¹ may be selected so as to provide an overalllength of the linker of between 2-100 atoms. Y¹ may be selected so thatthe overall length of the linker is between 5 and 30 atoms. Y¹ may beselected so that the overall length of linker is 15-25 atoms. Y¹ may beselected so that the overall length of linker is between about 17 andabout 19 atoms.

In some aspects, Y¹ may be an amino alkanoic acid, such as:

where n=0 to 20 in some aspects 1-10, in some aspects, 1-5, and in someaspects, 1 and in some aspects, 2.

In some aspects, Y¹ may be an alkanoic diacid, such as:

where n=0 to 20 in some aspects 1-10, in some aspects, 1-5, and in someaspects, 1 and in some aspects, 2.

In some aspects, Y¹ may be a polyglycine, such as:

where n=0 to 10, in some aspects 1-10, in some aspects, 1-5, and in someaspects, 1 and in some aspects, 2.

In some aspects, Y¹, X¹—Y¹, Y¹—Z, and X¹—Y¹—Z may be selected from thegroup consisting of:

where m, n, j and k are each independently 0 to 30. In some aspectsn=1-10, in some aspects, n=1-5. In some aspects, the lower limit of therange of values for n is selected from the group consisting of 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and 20, andthe upper limit for the range of values for n is selected from the groupconsisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. N may be 1. Nmay be 2. N may be 3. N may be 4. N may be 5. N may be 6. In someaspects m=1-10, in some aspects, m=1-5. In some aspects, the lower limitof the range of values for m is selected form the group consisting of 0,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and20, and the upper limit for the range of values for m is selected fromthe group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. M maybe 1. M may be 2. M may be 3. M may be 4. M may be 5. M may be 6. Insome aspects j=1-10, in some aspects, j=1-5. In some aspects, the lowerlimit of the range of values for j is selected from the group consistingof 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,and 20, and the upper limit for the range of values for j is selectedfrom the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. Jmay be 1. J may be 2. J may be 3. J may be 4. J may be 5. J may be 6. Insome aspects k=1-10, in some aspects, k=1-5. In some aspects, the lowerlimit of the range of values for k is selected from the group consistingof 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,and 20, and the upper limit for the range of values for k is selectedfrom the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. Kmay be 1. K may be 2. K may be 3. K may be 4. K may be 5. K may be 6. Insome aspects, the overall length of Y¹ does not exceed 200 atoms. Insome aspects, the overall length of Y¹ does not exceed 150 atoms. Insome aspects, the overall length of Y¹ does not exceed 100 atoms. Insome aspects, the overall length of Y¹ does not exceed 50 atoms. In someaspects, the range of overall chain length of Y¹ in numbers of atoms mayhave a lower limit selected from the group consisting of 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, and 60,and an upper limit selected from the group consisting of 5, 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, and 100. Insome aspects, the X¹Y¹Z linker may be identical to the above Y¹ groups.In some aspects, the wavy line connects to the X¹ group. In someaspects, the parallel lines connect to the X¹ group. In some aspects,the wavy line connects to the Z group. In some aspects, the parallellines connect to the Z group. In some aspects, the wavy line connects tothe side chain of CLκ-K⁸⁰. In some aspects, the parallel lines connectto the side chain of CLκ-K⁸⁰. In some aspects, the wavy line connects tothe Effector Moiety. In some aspects, the parallel lines connect toEffector Moiety. In some aspects, one of the wavy or parallel lines arepoints of attachment to a cleavable portion of the linker (φ).

Leaving Groups

Z* may be selected so as to enable a specific directional covalentlinking strategy to a lysine side chain on the antibody. For example, Zmay be COOH, or another similarly reactive electrophile to react withthe ε-amino of the surface lysine side chains using one of a number ofpossible amide bond formation strategies.

In some aspects, Z* may be used to form an active ester. Active estersconnect to amines, and can thus conjugate to the ε-amino of a lysineside chain of the antibody. The Z carboxyl function to enable theformation of the active ester will be present at the terminus of Ygroup. The alcoholic or phenolic function of the active ester acts as aleaving group Z* during the conjugation reaction, enabling connectionwith the lysine side chain on the antibody via generation of an amide.

In some embodiments, the Z* group comprises a structure of the formula:

where R′ is an aliphatic or aromatic group.

In some embodiments, the Z* group is of the formula:

where R′=any of F, Cl, Br or I, nitro, cyano, trifluoromethyl, alone orin combination, and may be present in an amount of between 1 and 5. Insome embodiments, R¹ may be a halogen, and 4 or 5 halogen atoms may bepresent. In some embodiments, there may be 4 R¹ atoms. In someembodiments, there may be 5 R¹ atoms. In some embodiments, Z* may betetrafluorophenyl. In some embodiments, Z* may comprise the formula:

Pentafluorophenyl

wherein the parallel line represents the point of attachment to the Y¹portion of the linker.

In some embodiments, Z* may comprise the formula:

wherein R³, R⁴, R⁵, R⁶ and R⁷ are each independently selected from thegroup consisting of F, CL, H and the formula CR⁸R⁹R¹⁰, such that no morethan two of R³, R⁴, R⁵, R⁶ and R⁷ are H, and one of R³, R⁴, R⁵, R⁶ andR⁷ is CR⁸R⁹R¹⁰, and R⁸, R⁹, and R¹⁰ are each independently selected fromthe group consisting of F, Cl and H such that no more than one of R⁸, R⁹and R¹⁰ may be H, and wherein the parallel line represents the point ofattachment to the Y¹ portion of the linker. In some aspects, the groupCR⁸R⁹R¹⁰ is located at one of R⁴, R⁵ or R⁶. In some aspects, the groupCR⁸R⁹R¹⁰ is located at R⁵

In some aspects, R³, R⁴, R⁵, R⁶ and R⁷ are each independently selectedfrom the group consisting of F, Cl, H and the formula CR⁸R⁹R¹⁰, suchthat no more than one of R³, R⁴, R⁵, R⁶ and R⁷ is H, and one of R³, R⁴,R⁵, R⁶ and R⁷ is CR⁸R⁹R¹⁰. In some aspects, R³, R⁴, R⁵, R⁶ and R⁷ areeach independently selected from the group consisting of F, Cl, and theformula CR⁸R⁹R¹⁰, and one is CR⁸R⁹R¹⁰.

In some aspects, R³, R⁴, R⁶ and R⁷ are each F. In some aspects, R⁸, R⁹,and R¹⁰ are each independently selected from the group consisting of Fand Cl. In some aspects, R⁸, R⁹, and R¹⁰ are each F.

In some embodiments, Z* may comprise the formula:

2,3,5,6-tetrafluoro-4-(trifluoromethyl)phenylwherein the parallel line represents the point of attachment to the Y¹portion of the linker.

In some aspects, the Z* group is of the formula:

where R′=any of F, Cl, Br or I, nitro, cyano, trifluoromethyl, alone orin combination, and h=1, 2, 3, 4, or 5. In some embodiments, R¹ may be ahalogen. In some embodiments, R¹ is F or Cl, and h=4 or 5. In someembodiments, R¹ is F or Cl, and h=5. In some embodiments, R¹ is F, andh=2, 3, 4 or 5. In some embodiments, R¹ is F, and h=3, 4 or 5. In someembodiments, R¹ is F, and h=4 or 5. In some embodiments, R¹ is F, andh=5. In some aspects, Z* may be selected from the group consisting of:

In some aspects, Z* may be selected from the group consisting of:

In some aspects, Z* may be selected from the group consisting of:

In some aspects, Z* may be selected from the group consisting of:

For such active esters, the leaving group is Z* and the Z group itselfis the carbonyl attached to the Y¹ group. When reacted with theantibody, the Z* group forms an amide, as shown below,

In some embodiments, Z is

In some embodiments, the Z* group comprises a squarate ester such as

wherein R=aliphatic group or substituted aromatic and may be selectedfrom the group consisting of:

In some embodiments, the Z group comprises a Maleimide group:

In some aspects, the X¹*Y¹Z* linker comprises a Maleimide-PEG-PFP esterof the structure:

where n=1 to 12. In some aspects, n=1 to 5. In some aspects n=2. In someaspects n=1.

In some aspects, the X¹*Y¹Z* linker comprises a structure selected fromthe group consisting of:

where m, n and j are each independently 0 to 30, R1 is F and h=2, 3, 4,or 5. In some aspects n=1-10, in some aspects, n=1-5. In some aspects,the lower limit of the range of values for n is selected from the groupconsisting of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, and 20, and the upper limit for the range of values for n isselected from the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,and 30. N may be 1. N may be 2. N may be 3. N may be 4. N may be 5. Nmay be 6. In some aspects m=1-10, in some aspects, m=1-5. In someaspects, the lower limit of the range of values for m is selected formthe group consisting of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, and 20, and the upper limit for the range ofvalues for m is selected from the group consisting of 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, and 30. M may be 1. M may be 2. M may be 3. M may be 4.M may be 5. M may be 6. In some aspects j=1-10, in some aspects, j=1-5.In some aspects, the lower limit of the range of values for j isselected from the group consisting of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, and 20, and the upper limit for therange of values for j is selected from the group consisting of 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, and 30. J may be 1. J may be 2. J may be 3. Jmay be 4. J may be 5. J may be 6. In some aspects k=1-10, in someaspects, k=1-5. In some aspects, the lower limit of the range of valuesfor k is selected from the group consisting of 0, 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and 20, and the upperlimit for the range of values for k is selected from the groupconsisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. K may be 1. Kmay be 2. K may be 3. K may be 4. K may be 5. K may be 6. In someaspects, the overall length of Y¹ does not exceed 200 atoms. In someaspects, the overall length of Y¹ does not exceed 150 atoms. In someaspects, the overall length of Y¹ does not exceed 100 atoms. In someaspects, the overall length of Y¹ does not exceed 50 atoms. In someaspects, the range of overall chain length of Y¹ in numbers of atoms mayhave a lower limit selected from the group consisting of 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, and 60,and an upper limit selected from the group consisting of 5, 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, and 100.

In some aspects the MAC comprises a X¹Y¹Z linker of the formula:

In some aspects, the X¹*Y¹Z* linker comprises aPEG-bis-pentafluorophenyl ester of the formula:

where n=1 to 25. In some aspects n=1 to 20. In some aspects n=1 to 10.In some aspects n=4. N=3, In some aspects n=1.

In some aspects the MAC comprises 2 peptides conjugated per antibody. Insome aspects, one peptide is conjugated at each of the 2 CLκ-K⁸⁰residues of the antibody or antigen binding fragment thereof.

In some aspects, the polypeptide of the invention comprises a formulaselected from the group consisting of:

wherein -KH- is a covalent link to the side chain of K⁵ of SEQ ID NO:98,Effector Moiety-LR is a covalent link to the Effector Moiety, and m, nand j are each independently 0-30. In some aspects n=1-10, in someaspects, n=1-5. In some aspects, the lower limit of the range of valuesfor n is selected from the group consisting of 0, 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and 20, and the upperlimit for the range of values for n is selected from the groupconsisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. N may be 1. Nmay be 2. N may be 3. N may be 4. N may be 5. N may be 6. In someaspects m=1-10, in some aspects, m=1-5. In some aspects, the lower limitof the range of values for m is selected form the group consisting of 0,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and20, and the upper limit for the range of values for m is selected fromthe group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. M maybe 1. M may be 2. M may be 3. M may be 4. M may be 5. M may be 6. Insome aspects j=1-10, in some aspects, j=1-5. In some aspects, the lowerlimit of the range of values for j is selected from the group consistingof 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,and 20, and the upper limit for the range of values for j is selectedfrom the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. Jmay be 1. J may be 2. J may be 3. J may be 4. J may be 5. J may be 6. Insome aspects, the overall length of Y¹ does not exceed 200 atoms. Insome aspects, the overall length of Y¹ does not exceed 150 atoms. Insome aspects, the overall length of Y¹ does not exceed 100 atoms. Insome aspects, the overall length of Y¹ does not exceed 50 atoms. In someaspects, the range of overall chain length of Y¹ in numbers of atoms mayhave a lower limit selected from the group consisting of 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, and 60,and an upper limit selected from the group consisting of 5, 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, and 100.

In some aspects, the linker is selected from the group consisting of

Cleavable Linkers

In some aspects, the invention provides for MACs as described hereincomprising “non-cleavable” linkers. In other aspects, the inventionprovides for MACs comprising “cleavable” linkers. The term “cleavablelinker” is used herein to describe a rapidly cleaved linker that isdesigned to be degraded by intracellular or extracellular enzymes orwhen subjected to changes in pH or redox environment so as to releasethe cargo at the desired location. For example, cleavable linkers may bepreferentially stable in plasma, blood or serum, and less stable inintracellular environments.

Cleavable linkers can be formed by adding a cleavable portion (φ) to theY¹ portion of the linker (or P¹ portion, where the linker is for acatalytic antibody combining site). Accordingly, the linkers would takethe formula X¹-φ-Y¹—Z, X¹-φ-Y¹—Z*, and P¹-φ-Q¹-W¹.

A representative example of a cleavable portion of a linker isvaline-citrulline p-aminobenzyl carbamate (VitCitABC) that is cleaved byintracellular proteases such as cathepsin B.

where the wavy line typically indicates the point of attachment to theY¹ (or Q¹) portion of the linker, and the parallel line represents thepoint of attachment to the X¹ (or P¹) portion of the linker, or even tothe Effector Moiety itself. In some aspects, of course, the wavy linemay indicate the point of attachment to the X¹ or P¹ linker portion (orEffector Moiety), and the parallel line may indicate the point ofattachment to the Y¹ or Q¹ portion of the linker.

Accordingly, in some aspects, the invention provides for linker of theformula:

where m, n and j are each independently 0 to 30, R1 is F and h=2, 3, 4,or 5. In some aspects n=1-10, in some aspects, n=1-5. In some aspects,the lower limit of the range of values for n is selected from the groupconsisting of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, and 20, and the upper limit for the range of values for n isselected from the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,and 30. N may be 1. N may be 2. N may be 3. N may be 4. N may be 5. Nmay be 6. In some aspects m=1-10, in some aspects, m=1-5. In someaspects, the lower limit of the range of values for m is selected formthe group consisting of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, and 20, and the upper limit for the range ofvalues for m is selected from the group consisting of 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, and 30. M may be 1. M may be 2. M may be 3. M may be 4.M may be 5. M may be 6. In some aspects j=1-10, in some aspects, j=1-5.In some aspects, the lower limit of the range of values for j isselected from the group consisting of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, and 20, and the upper limit for therange of values for j is selected from the group consisting of 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, and 30. J may be 1. J may be 2. J may be 3. Jmay be 4. J may be 5. J may be 6. In some aspects k=1-10, in someaspects, k=1-5. In some aspects, the lower limit of the range of valuesfor k is selected from the group consisting of 0, 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and 20, and the upperlimit for the range of values for k is selected from the groupconsisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. K may be 1. Kmay be 2. K may be 3. K may be 4. K may be 5. K may be 6. In someaspects, the overall length of Y¹ does not exceed 200 atoms. In someaspects, the overall length of Y¹ does not exceed 150 atoms. In someaspects, the overall length of Y¹ does not exceed 100 atoms. In someaspects, the overall length of Y¹ does not exceed 50 atoms. In someaspects, the range of overall chain length of Y¹ in numbers of atoms mayhave a lower limit selected from the group consisting of 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, and 60,and an upper limit selected from the group consisting of 5, 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, and 100.

Use of Auristatin-Based Payloads

Auristatin-based effector moieties are also useful in connection withthe targeted conjugation technology of the present invention when usedin conjunction with the appropriate linker technology. Specifically,useful payloads include those disclosed in PCT/IB2012/056224 includingall pharmaceutically acceptable salts, hydrates and free base forms.

Accordingly, the following effector moieties and linkers may be used inaspects of the invention:

or a pharmaceutically acceptable salt or solvate thereof, wherein,independently for each occurrence,

W² is

R¹¹ is

Y² is —C₂-C₂₀ alkylene-, —C₂-C₂₀ heteroalkylene-; —C₃-C₈ carbocyclo-,-arylene-, —C₃-C₈heterocyclo-, —C₁-C₁₀alkylene-arylene-,-arylene-C₁-C₁₀alkylene-, —C₁-C₁₀alkylene-(C₃-C₈carbocyclo)-,-(C₃-C₈carbocyclo)-C₁-C₁₀alkylene-, —C₁-C₁₀alkylene-(C₃-C₈heterocyclo)-or —(C₃-C₈ heterocyclo)-C₁-C₁₀alkylene-;

Z² is

R¹² is hydrogen, C₁-C₈ alkyl or C₁-C₈ haloalkyl;

R^(13A) and R^(13B) are either of the following:

-   -   (i) R^(13A) is hydrogen, C₁-C₈ alkyl, C₁-C₈ haloalkyl, C₃-C₈        carbocyclyl, C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl, aralkyl        or halogen; and        -   R^(13B) is C₁-C₈ alkyl, C₁-C₈ haloalkyl, C₃-C₈ carbocyclyl,            C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl or aralkyl or            halogen; or    -   (ii) R^(13A) and R^(13B) taken together are C₂-C₈ alkylene or        C₁-C₈ heteroalkylene;

R^(14A) and R^(14B) are either of the following:

-   -   (i) R^(14A) is hydrogen, C₁-C₈ alkyl, C₁-C₈ haloalkyl, C₃-C₈        carbocyclyl, C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl or        aralkyl; and        -   R^(14B) is hydrogen, C₁-C₈ alkyl, C₁-C₈ haloalkyl, C₃-C₈            carbocyclyl, C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl or            aralkyl; or    -   (ii) R^(14A) and R^(14B) taken together are C₂-C₈ alkylene or        C₁-C₈ heteroalkylene;

R¹⁵ is

C₁-C₁₀ heterocyclyl, C₃-C₈ carbocycly and C₆-C₁₄ aryl optionallysubstituted with 1, 2, 3, 4 or 5 groups independently selected from thegroup consisting of —C₁-C₈ alkyl, —C₁-C₈ alkyl-N(R′)₂, —C₁-C₈alkyl-C(O)R′, —C₁-C₈ alkyl-C(O)OR′—O—(C₁-C₈ alkyl), —C(O)R′, —OC(O)R′,—C(O)OR′, —C(O)N(R′)₂, —NHC(O)R′, —S(O)₂R′, —S(O)R′, —OH, halogen, —N₃,—N(R′)₂, —CN, —NHC(═NH)NH₂, —NHCONH₂, —S(═O)₂R′ and —SR′, wherein eachR′ is independently selected from the group consisting of hydrogen,C₁-C₈ alkyl and unsubstituted aryl, or two R′ can, together with thenitrogen to which they are attached, form a C₁-C₁₀ heterocyclyl;

or R¹⁵ is

optionally substituted with 1, 2, 3, 4 or 5 groups independentlyselected from the group consisting of C₁-C₈ alkyl, —C₁-C₈ alkyl-N(R′)₂,—C₁-C₈ alkyl-C(O)R′, —C₁-C₈ alkyl-C(O)OR′, —O—(C₁-C₈ alkyl), —C(O)R′,—OC(O)R′, —C(O)OR′, —C(O)N(R′)₂, —NHC(O)R′, —S(O)₂R′, —S(O)R′, —OH,halogen, —N₃, —N(R′)₂, —CN, —NHC(═NH)NH₂, —NHCONH₂, —S(═O)₂R′, —SR′ andarylene-R′, wherein each R′ is independently selected from the groupconsisting of hydrogen, C₁-C₈ alkyl, C₁-C₈heterocyclyl,C₁-C₁₀alkylene-C₃-C₈heterocyclyl and aryl, or two R′ can, together withthe nitrogen to which they are attached, form a C₁-C₁₀ heterocyclyl;

R¹⁶ is hydrogen, —C₁-C₈ alkyl, —C₂-C₈ alkenyl, —C₂-C₈ alkynyl or —C₁-C₈haloalkyl;

R²² is hydrogen, C₁-C₄ alkyl, C₁-C₁₀ heterocyclyl or C₆-C₁₄ aryl;

R²³ is C₁-C₁₀ heterocyclyl; and

R¹⁷ is independently selected for each occurrence from the groupconsisting of F, Cl, I and Br;

R²⁰ is -aryl, —C₁-C₁₀alkylene-aryl, where aryl on R¹⁰ comprising aryl issubstituted with [R¹⁷]_(h);

h is 5; and

X is O or S;

provided that when R^(13A) is hydrogen X is S.

In some aspects, the effector moieties may be selected from Table 73. Insome aspects, the effector moiety is Toxin #54. In some aspects, theeffector moiety is Toxin #115. In some aspects, the effector moiety isToxin #69.

In some aspects, the Effector Moiety when conjugated to a linker of theinvention comprises a formula selected from the group consisting of

Effector Moieties conjugated to linkers useful in connection with thepresent invention include auristatin-based toxin-linkers such as thosedisclosed in PCT/IB2012/056224. In some aspects, the toxin-linkers ofthe invention may be selected from the group consisting of

Methods of Conjugation

In some aspects, the invention provides for a method of preparing amultifunctional antibody conjugate (MAC) comprising an antibody orantigen binding portion, the antibody being covalently conjugated to atleast one Effector Moiety through a linker attached to a side chain ofK⁵ of SEQ ID NO:98 (or SEQ ID herein disclosed falling within the scopeof SEQ ID NO:98), or to a side chain of residue K on an antibodyconstant domain wherein the position of K corresponds with residue 77 ofSEQ ID NO:6, or residue 185 of a constant light domain according toKabat numbering;

said method comprising: covalently attaching the Effector Moiety to alinker terminating in a leaving group Z* of the formula:

where R¹ is any of F, Cl, Br or I, nitro, cyano, trifluoromethyl, aloneor in combination, and h=1, 2, 3, 4, or 5, and reacting the EffectorMoiety-linker-leaving group complex so formed with the antibody at amolar ratio of between about 3.5:1 to about 4.5:1 of EffectorMoiety:antibody. In some aspects, the molar ratio is about 3.7:1 toabout 4.3:1. In some embodiments, R¹ may be a halogen. In someembodiments, R¹ is F or Cl, and h=4 or 5. In some embodiments, R¹ is For Cl, and h=5. In some embodiments, R¹ is F, and h=2, 3, 4 or 5. Insome embodiments, R¹ is F, and h=3, 4 or 5. In some embodiments, R¹ isF, and h=4 or 5. In some embodiments, R¹ is F, and h=5. In some aspects,Z* may be selected from the group consisting of:

R¹ may be present in an amount of between 3 and 5. There may be 3 R¹groups. R¹ may be present in an amount of between 4 and 5. There may be4 R¹ groups. There may be 5 R¹ groups. R¹ may be fluorine. R¹ may bechlorine. R¹ may be bromine. The leaving group may comprise the formula:

In some aspects, the invention provides for methods of producing a MAC,wherein the MAC comprises an antibody, or fragment thereof, covalentlylinked to at least one Effector Moiety that binds an additional target(such as peptide, small molecule, aptamer, nucleic acid molecule, orprotein), characterised in that Effector Moiety comprises a linker witha PFP leaving group capable of reacting with the ε-amino of surfacelysine residues of the antibody. In some aspects, the invention providesfor a process for conjugating an Effector Moiety (such as a peptide) toa CL domain of the invention comprising SEQ ID NO:98, comprisingconjugating the Effector Moiety with a linker comprising a leaving groupof the formula:

where R¹ is any of F, Cl, Br or I, nitro, cyano, trifluoromethyl, aloneor in combination, and may be present in an amount of between 1 and 5and reacting the leaving group with the side chain of K⁵ of SEQ IDNO:98.

In some aspects, the method comprises combining an antibody or antigenbinding portion thereof with an Effector Moiety, wherein the EffectorMoiety is covalently attached to a linker comprising a PFP leavinggroup.

In some aspects, the molar ratio of Effector Moiety:antibody is betweenabout 2.5 and about 4.6:1. In some aspects of the invention, the molarratio is about 3.7:1, and about 4.3:1. In some aspects of the invention,the molar ratio of Effector Moiety:antibody is about 4:1. In someaspects, the molar ratio is between about 2:1 and about 7:1. In someaspects, the molar ratio is between about 3:1 and about 6:1. In someaspects, the molar ratio is between about 3:1 and about 7:1. In someaspects, the molar ratio is between about 3:1 and about 5:1.

In aspects of the invention where it is desirable to have less than 1.5conjugations per antibody (such as where a single Effector Moiety isrequired) the molar ratio may be between about 1:1 and about 6:1,wherein the buffer comprises HEPES at a concentration of at least 0.02M.The concentration of HEPES may be between about 0.1M and about 1M. Theconcentration of HEPES may between about 0.1M and about 0.5M. In aspectsof the invention where it is desirable to have less than 1.5conjugations per antibody (such as where a single Effector Moiety isrequired) the molar ratio may be between about 1:1 and about 3:1.

In some aspects, the preferred molar ratio is a range with a lower limitselected from the group consisting of about 1, about 1.2, about 1.4,about 1.5, about 1.6, about 1.8, about 2, about 2.2, about 2.4, about2.5, about 2.6, about 2.8, about 3, about 3.2, about 3.3, about 3.4,about 3.5, about 3.6, about 3.7, about 3.8, about 3.9, about 4.0, about4.1, about 4.2, about 4.3, about 4.4. about 4.5, about 4.6, about 4.7,about 4.8, about 4.9, about 5, about 5.2, about 5.4, about 5.5, about5.6, about 5.8, about 6, about 6.2, about 6.4, about 6.5, about 6.6,about 6.8, about 7, about 7.3, about 7.5, about 7.7, about 8, about 8.5,about 9, about 9.5, and about 10 to 1, and an upper limit selected fromthe group consisting of about 1.5, about 1.6, about 1.8, about 2, about2.2, about 2.4, about 2.5, about 2.6, about 2.8, about 3, about 3.2,about 3.3, about 3.4, about 3.5, about 3.6, about 3.7, about 3.8, about3.9, about 4.0, about 4.1, about 4.2, about 4.3, about 4.4. about 4.5,about 4.6, about 4.7, about 4.8, about 4.9, about 5, about 5.2, about5.4, about 5.5, about 5.6, about 5.8, about 6, about 6.2, about 6.4,about 6.5, about 6.6, about 6.8, about 7, about 7.3, about 7.5, about7.7, about 8, about 8.5, about 9, about 9.5, about 10, and about 15 to1.

In some aspects, the invention further comprises conjugating theEffector Moiety and protein together for at least about 30 mins. In someaspects, the duration is at least about 60 mins. In some aspects, theduration is at least about 2 hrs. In some aspect, the invention furthercomprises conjugating the Effector Moiety and antibody at between about4° C. and about 40° C. In some aspect, the invention further comprisesconjugating the Effector Moiety and antibody at between about 10° C. andabout 30° C. In some aspect, the invention further comprises conjugatingthe Effector Moiety and antibody at between about 15° C. and about 30°C. In some aspects, the reaction is conducted at about 18° C. to about25° C. In some aspects, the reaction is conducted at about 22° C. Insome aspects, the reaction is conducted at about room temperature.

In some aspects, the conjugation reaction takes place at between aboutpH 6.5 and about pH 8.0. In some aspects, the conjugation reaction takesplace at between about pH 6.75 and about pH 8.0. In some aspects, theconjugation reaction takes place at about pH 7.7. In some aspects, theconjugation reaction takes place at about pH 7. In some aspects, theconjugation reaction takes place at about pH 7.2. In some aspects, theconjugation reaction takes place at about pH 7.5. In some aspects, theconjugation reaction takes place at between a range of pH values, whoselower limit is selected from the group consisting of 5.5, 6, 6.1, 6.2,6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6,7.7, 7.8, 7.9 and 8, and whose upper limit is selected from the groupconsisting of 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5,7.6, 7.7, 7.8, 7.9, 8.0, 8.5, and 9.

In some aspects, the pH may be below 6.5; this may be particularlyuseful in applications were less than about 1.5 conjugations perantibody are required. In some aspects, the pH is between about 5.5 andabout 6.5.

In some aspects, the salt concentration may be below about 0.2M. Thesalt may be a halide salt (F, Cl, Br, I) and may comprise a metal suchas Li, Na, K, Be, Mg, Ca. The salt may be NaCl. The salt may be KCl.Salt concentrations of above about 0.1M may be used to limit the rateand/or number of conjugations per antibody. The salt concentration maybe between about 0 and about 0.1M. The salt concentration may be betweenabout 0 and about 0.5M. The salt concentration may be between about 0and about 0.3M.

In some aspects, the method of the invention comprises formulating theantibody or antigen binding portion thereof in a formulation buffer atabout pH 5.5. The formulation buffer may be sodium acetate and trehalosebuffer. This buffer has the advantage of not containing any primaryamines, and lends itself well to pH adjustment. The antibody may bepresent in an amount of about 15 to about 25 mg.ml⁻¹. In some aspects,the antibody may be present at an amount of 20 mg.ml⁻¹.

The pH of the formulation buffer may be adjusted to about pH 7.2 toabout pH 8.0; in some embodiments, the formulation buffer may beadjusted to pH 7.7. The pH of the formulation buffer may be adjustedwith a phosphate buffer. The phosphate buffer may be at a concentrationof between about 40 mM and about 80 mM. The phosphate buffer may be at aconcentration of between about 10 mM and about 200 mM.

In some aspects, the concentration of antibody during the conjugationreaction with the Effector Moiety/linker and leaving group Z* may be ina range where the lower limit of the range is selected from about 5,about 6, about 7, about 8, about 9, about 10, about 15, about 20, about30, and about 40 mg.ml⁻¹, and the upper limit of the range is selectedform the group consisting of about 7, about 8, about 9, about 10, about15, about 20, about 30, about 40, about 50, about 60, about 70, about80, about 90, about 100, about 150, about 200, about 500 mg.ml⁻¹.

The Effector Moiety may be reconstituted at a concentration of at leastabout 2 mg.ml⁻¹. The Effector Moiety may be reconstituted at aconcentration of about 5 to about 20 mg.ml⁻¹ in diluted propylene glycolprior to use and, in some embodiments, may be at a concentration of 10mg.ml⁻¹.

The conjugation reaction may be performed by combining the antibody orantigen binding portion thereof and the Effector Moiety at a molar ratioof 4 moles Effector Moiety to 1 mole of antibody and incubated at about18° C. to about 25° C. for about 2 to about 24 hrs. In some embodiments,the conjugation reaction between antibody and Effector Moiety is at roomtemperature for 2 hrs. In some embodiments, the conjugation reaction isfor at least about 2 hrs. In some embodiments, the conjugation reactionis for at least about 30 mins.

The reaction may be quenched and adjusted to about pH 5.0 to about pH6.0. In some embodiments, the quenched reaction may be adjusted to pH5.5. This may be accomplished using a succinate and glycine buffer at,for example, about pH 4.0. This buffer has advantages over other morecommon buffers such as TRIS, or other amino-acid buffers. The succinateassists in limiting aggregation and precipitation during diafiltration,which can be stressful on the conjugated molecule, and glycine containsan additional primary amine.

The reaction may be concentrated and unreacted Effector Moiety, relatedspecies (such as peptide where the linker was hydrolyzed by reactionwith water solvent) and other unreacted elements of the reaction mixture(such as PFP) may be removed by diafiltration, for example, using a 50kDa membrane or size exclusion chromatography into a succinate, glycine,sodium chloride, and trehalose buffer, pH 5.5 at 30 mg.ml⁻¹.

In some aspects, the method may comprise conjugating an Effector Moietyto CLκ-K⁸⁰. In some aspects, the invention comprises conjugating aEffector Moiety to an Ig domain, comprising mutating the CLλ so as tocomprise a SEQ ID NO:98 on the EF connecting chain loop betweenβ-strands E and F, attaching to the Effector Moiety a linker comprisinga leaving group Z* as herein defined, and reacting said EffectorMoiety-linker-leaving group complex with the side chain of K⁵ of SEQ IDNO:98.

Pharmaceutical Compositions of the Invention

The invention provides a pharmaceutical composition comprising the MACand a pharmaceutically acceptable carrier. As used herein,“pharmaceutically acceptable carrier” includes any and all solvents,dispersion media, coatings, antibacterial and antifungal agents,isotonic and absorption delaying agents, and the like that arephysiologically compatible. Examples of pharmaceutically acceptablecarriers include one or more of water, saline, phosphate bufferedsaline, dextrose, glycerol, ethanol and the like, as well ascombinations thereof, and may include isotonic agents, for example,sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride inthe composition. Pharmaceutically acceptable substances such as wettingor minor amounts of auxiliary substances such as wetting or emulsifyingagents, preservatives or buffers, which enhance the shelf life oreffectiveness of the antibody or antibody portion.

The compositions of this invention may be in a variety of forms. Theseinclude, for example, liquid, semi-solid and solid dosage forms, such asliquid solutions (e.g., injectable and infusible solutions), dispersionsor suspensions, tablets, pills, powders, liposomes and suppositories.The preferred form depends on the intended mode of administration andtherapeutic application. Typical preferred compositions are in the formof injectable or infusible solutions, such as compositions similar tothose used for passive immunization of humans with antibodies ingeneral. The preferred mode of administration is parenteral (e.g.intravenous, subcutaneous, intraperitoneal, intramuscular). In apreferred embodiment, the antibody is administered by intravenousinfusion or injection. In another preferred embodiment, the antibody isadministered by intramuscular or subcutaneous injection.

The pharmaceutical composition may further comprise another component,such as an anti-tumour agent or an imaging reagent. Another aspect ofthe present invention provides kits comprising MACs of the invention andpharmaceutical compositions comprising these antibodies. A kit mayinclude, in addition to the MAC or pharmaceutical composition,diagnostic or therapeutic agents. A kit may also include instructionsfor use in a diagnostic or therapeutic method. In some embodiments, thekit includes the antibody or a pharmaceutical composition thereof and adiagnostic agent. In other embodiments, the kit includes the antibody ora pharmaceutical composition thereof and one or more therapeutic agents,such as an additional antineoplastic agent, anti-tumour agent orchemotherapeutic agent.

These agents and compounds of the invention can be combined withpharmaceutically acceptable vehicles such as saline, Ringer's solution,dextrose solution, and the like. The particular dosage regimen, i.e.,dose, timing and repetition, will depend on the particular individualand that individual's medical history.

Acceptable carriers, excipients, or stabilizers are nontoxic torecipients at the dosages and concentrations employed, and may comprisebuffers such as phosphate, citrate, and other organic acids; salts suchas sodium chloride; antioxidants including ascorbic acid and methionine;preservatives (such as octadecyldimethylbenzyl ammonium chloride;hexamethonium chloride; benzalkonium chloride, benzethonium chloride;phenol, butyl or benzyl alcohol; alkyl parabens, such as methyl orpropyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; andm-cresol); low molecular weight (less than about 10 residues)polypeptides; proteins, such as serum albumin, gelatin, or Igs;hydrophilic polymers such as polyvinylpyrrolidone; amino acids such asglycine, glutamine, asparagine, histidine, arginine, or lysine;monosaccharides, disaccharides, and other carbohydrates includingglucose, mannose, or dextrins; chelating agents such as EDTA; sugarssuch as sucrose, mannitol, trehalose or sorbitol; salt-formingcounter-ions such as sodium; metal complexes (e.g., Zn-proteincomplexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ orpolyethylene glycol (PEG).

Liposomes containing compounds of the invention are prepared by methodsknown in the art, such as described in U.S. Pat. Nos. 4,485,045 and4,544,545. Liposomes with enhanced circulation time are disclosed inU.S. Pat. No. 5,013,556. Particularly useful liposomes can be generatedby the reverse phase evaporation method with a lipid compositioncomprising phosphatidylcholine, cholesterol and PEG-derivatizedphosphatidylethanolamine (PEG-PE). Liposomes are extruded throughfilters of defined pore size to yield liposomes with the desireddiameter.

The active ingredients may also be entrapped in microcapsules prepared,for example, by coacervation techniques or by interfacialpolymerization, for example, hydroxymethylcellulose orgelatin-microcapsules and poly-(methylmethacrylate) microcapsules,respectively, in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules) or in macroemulsions. Such techniques are disclosed inRemington, The Science and Practice of Pharmacy, 20th Ed., MackPublishing (2000).

Sustained-release preparations may be prepared. Suitable examples ofsustained-release preparations include semi-permeable matrices of solidhydrophobic polymers containing the antibody, which matrices are in theform of shaped articles, e.g., films, or microcapsules. Examples ofsustained-release matrices include polyesters, hydrogels (for example,poly(2-hydroxyethyl-methacrylate), or ′poly(vinylalcohol)), polylactides(U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and 7ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradablelactic acid-glycolic acid copolymers such as the LUPRON DEPOT™(injectable microspheres composed of lactic acid-glycolic acid copolymerand leuprolide acetate), sucrose acetate isobutyrate, andpoly-D-(−)-3-hydroxybutyric acid.

The formulations to be used for in vivo administration must be sterile.This is readily accomplished by, for example, filtration through sterilefiltration membranes. Therapeutic compounds of the invention aregenerally placed into a container having a sterile access port, forexample, an intravenous solution bag or vial having a stopper pierceableby a hypodermic injection needle.

Suitable emulsions may be prepared using commercially available fatemulsions, such as Intralipid™, Liposyn™, Infonutrol™, Lipofundin™ andLipiphysan™. The active ingredient may be either dissolved in apre-mixed emulsion composition or alternatively it may be dissolved inan oil (e.g., soybean oil, safflower oil, cottonseed oil, sesame oil,corn oil or almond oil) and an emulsion formed upon mixing with aphospholipid (e.g., egg phospholipids, soybean phospholipids or soybeanlecithin) and water. It will be appreciated that other ingredients maybe added, for example glycerol or glucose, to adjust the tonicity of theemulsion. Suitable emulsions will typically contain up to 20% oil, forexample, between 5 and 20%. The fat emulsion can comprise fat dropletsbetween 0.1 and 1.0 μm, particularly 0.1 and 0.5 μm, and have a pH inthe range of 5.5 to 8.0.

The emulsion compositions can be those prepared by mixing a compound ofthe invention with Intralipid™ or the components thereof (soybean oil,egg phospholipids, glycerol and water).

Compositions for inhalation or insufflation include solutions andsuspensions in pharmaceutically acceptable, aqueous or organic solvents,or mixtures thereof, and powders. The liquid or solid compositions maycontain suitable pharmaceutically acceptable excipients as set outabove. In some embodiments, the compositions are administered by theoral or nasal respiratory route for local or systemic effect.Compositions in preferably sterile pharmaceutically acceptable solventsmay be nebulised by use of gases. Nebulised solutions may be breatheddirectly from the nebulising device or the nebulising device may beattached to a face mask, tent or intermittent positive pressurebreathing machine. Solution, suspension or powder compositions may beadministered, preferably orally or nasally, from devices which deliverthe formulation in an appropriate manner.

Compounds and compositions of the invention may be used in conjunctionwith established treatments for the relevant indication. Examplesinclude 5-Fluorouracil, irinotecan, oxilaplatin, cetuximab, sunitinib,and rituximab for the treatment of angiogenic disorders in particular,especially cancer. Other examples include ranibizumab, infliximab,adalimumab, natalizumab, omalizumab, and palivizumab.

Therapeutic Methods of the Invention

Therapeutic methods are also provided by the invention. A therapeuticmethod comprises administering a compound or composition of theinvention to a subject in need thereof.

The invention provides for the use of compounds of the invention orpharmaceutical compositions of the invention in a method of inhibitingor reducing angiogenesis or for treating or preventing a disease orsymptom associated with an angiogenic disorder. The invention providesmethods of inhibiting or reducing angiogenesis or treating or preventinga disease or symptom associated with an angiogenic disorder comprisingadministering to a patient a therapeutically effective dose of compoundsand compositions of the invention. Also provided are methods ofdelivering or administering compounds and compositions of the inventionand methods of treatment using compounds and compositions of theinvention. Also provided are methods of treating cancer comprisingadministering to the subject a therapeutically effective amount of acompound or pharmaceutical composition according to the invention. Asused herein, an angiogenesis-mediated condition is a condition that iscaused by abnormal angiogenesis activity or one in which compounds thatmodulate angiogenesis activity have therapeutic use. Diseases andconditions that may be treated and/or diagnosed with compounds andcompositions of the invention include cancer, arthritis, hypertension,kidney disease, psoriasis, angiogenesis of the eye associated withocular disorder, infection or surgical intervention, maculardegeneration, diabetic retinopathy, and the like.

More specifically, examples of “cancer” when used herein in connectionwith the present invention include cancers of the lung (NSCLC and SCLC),the head or neck, the ovary, the colon, the rectum, the prostate, theanal region, the stomach, the breast, the kidney or ureter, the renalpelvis, the thyroid gland, the bladder, the brain, renal cell carcinoma,carcinoma of, neoplasms of the central nervous system (CNS), primary CNSlymphoma, non-Hodgkin's lymphoma, spinal axis tumours, carcinomas ofthe, oropharynx, hypopharynx, esophagus, pancreas, liver, gallbladderand bile ducts, small intestine, urinary tract; or lymphoma or acombination of one or more of the foregoing cancers. Still morespecifically, examples of “cancer” when used herein in connection withthe present invention include cancer selected from lung cancer (NSCLCand SCLC), breast cancer, ovarian cancer, colon cancer, rectal cancer,prostate cancer, cancer of the anal region, or a combination of one ormore of the foregoing cancers.

In other embodiments, pharmaceutical compositions of the inventionrelate to non-cancerous hyperproliferative disorders such as, withoutlimitation, age-related macular degeneration, restenosis afterangioplasty and psoriasis. In another embodiment, the invention relatesto pharmaceutical compositions for the treatment of a mammal thatrequires activation of IGF1R and/or Ang2, wherein the pharmaceuticalcomposition comprises a therapeutically effective amount of anactivating antibody of the invention and a pharmaceutically acceptablecarrier. Pharmaceutical compositions of the invention may be used totreat osteoporosis, frailty or disorders in which the mammal secretestoo little active growth hormone or is unable to respond to growthhormone.

As used herein, an “effective dosage” or “effective amount” of drug,compound, or pharmaceutical composition is an amount sufficient toaffect any one or more beneficial or desired results. For prophylacticuse, beneficial or desired results include eliminating or reducing therisk, lessening the severity, or delaying the outset of the disease,including biochemical, histological and/or behavioural symptoms of thedisease, its complications and intermediate pathological phenotypespresenting during development of the disease. For therapeutic use,beneficial or desired results include clinical results such as reducingtumour size, spread, vasculature of tumours, or one or more symptoms ofcancer or other diseases associated with increased angiogenesis,decreasing the dose of other medications required to treat the disease,enhancing the effect of another medication, and/or delaying theprogression of the disease of patients. An effective dosage can beadministered in one or more administrations. For purposes of thisinvention, an effective dosage of drug, compound, or pharmaceuticalcomposition is an amount sufficient to accomplish prophylactic ortherapeutic treatment either directly or indirectly. As is understood inthe clinical context, an effective dosage of a drug, compound, orpharmaceutical composition may or may not be achieved in conjunctionwith another drug, compound, or pharmaceutical composition. Thus, an“effective dosage” may be considered in the context of administering oneor more therapeutic agents, and a single agent may be considered to begiven in an effective amount if, in conjunction with one or more otheragents, a desirable result may be or is achieved.

An “individual” or a “subject” is a mammal, more preferably, a human.Mammals also include, but are not limited to, farm animals, sportanimals, pets, primates, and horses.

Advantageously, therapeutic administration of compounds of the inventionresults in decrease in angiogenesis and/or in the case of cancers,stabilized or reduced tumour volume. Preferably, tumour volume is atleast about 10% or about 15% lower than before administration of a MACof the invention. More preferably, tumour volume is at least about 20%lower than before administration of the MAC. Yet more preferably, tumourvolume is at least 30% lower than before administration of the MAC.Advantageously, tumour volume is at least 40% lower than beforeadministration of the MAC. More advantageously, tumour volume is atleast 50% lower than before administration of the MAC. Very preferably,tumour volume is at least 60% lower than before administration of theMAC. Most preferably, tumour volume is at least 70% lower than beforeadministration of the MAC.

Administration of compounds of the invention in accordance with themethod in the present invention can be continuous or intermittent,depending, for example, upon the recipient's physiological condition,whether the purpose of the administration is therapeutic orprophylactic, and other factors known to skilled practitioners. Theadministration of a compound of the invention may be essentiallycontinuous over a preselected period of time or may be in a series ofspaced doses.

Antibodies

The immunoglobulin (Ig) domain is a type of protein domain that consistsof a 2-layer sandwich of between 7 and 9 antiparallel β-strands arrangedin two β-sheets with a Greek key topology. A β-strand is a stretch ofpolypeptide chain typically 3 to 10 amino acids long with backbone in analmost fully extended conformation. B sheets consist of β-strandsconnected laterally by at least two or three backbone hydrogen bonds,forming a generally twisted, pleated sheet. The backbone switchesrepeatedly between the two β-sheets. Typically, the pattern is(N-terminal β-hairpin in sheet 1)-(β-hairpin in sheet 2)-(β-strand insheet 1)-(C-terminal β-hairpin in sheet 2). The cross-overs betweensheets form an “X”, so that the N- and C-terminal hairpins are facingeach other. Members of the Ig superfamily are found in hundreds ofproteins of different functions. Examples include antibodies, the giantmuscle kinase titin and receptor tyrosine kinases. Ig-like domains maybe involved in protein-protein and protein-ligand interactions

The α-helix is a right-handed coiled or spiral conformation of aminoacids, in which every backbone N—H group donates a hydrogen bond to thebackbone C═O group of the amino acid four residues earlier. Thissecondary structure is also sometimes called a classicPauling-Corey-Branson α-helix. Among types of local structure inproteins, the α-helix is the most regular and the most predictable fromsequence, as well as the most prevalent.

An immunoglobulin (Ig) is a tetrameric molecule. In a naturallyoccurring Ig, each tetramer is composed of 2 identical pairs ofpolypeptide chains, each pair having one “light” (about 25 kDa) and one“heavy” chain (about 50-70 kDa).

The amino-terminal portion of each chain includes a variable region, ofabout 100 to 110 or more amino acids primarily responsible for antigenrecognition. The carboxy-terminal portion of each chain defines aconstant region primarily responsible for effector function. Human lightchains are classified as κ and λ light chains. Heavy chains areclassified as α, 67 , ε, γ, and μ, and define the antibody's isotype asIgA, IgD, IgE, IgG, IgM, respectively. Within light and heavy chains,the variable and constant regions are joined by a “J” region of about 12or more amino acids, with the heavy chain also including a “D” region ofabout 10 more amino acids. The variable regions of each light/heavychain pair form the antibody binding site such that an intact Ig has 2binding sites.

Each domain in an antibody molecule has a similar structure of twoβ-sheets packed tightly against each other in a compressed antiparallelβ-barrel. This conserved structure is termed the immunoglobulin (Ig)fold. The Ig fold of constant domains contains a 3-stranded β sheetpacked against a 4-stranded β sheet, with each sheet separated bychains; these chains typically comprise α-helices, loops, turns, andshort, sharp turns between two β-sheets called β-hairpins.

Ig chains exhibit the same general structure of relatively conservedframework regions (FR) joined by 3 hypervariable regions, also calledcomplementarity determining regions or CDRs. The CDRs from the 2 chainsof each pair are aligned by the framework regions, enabling binding to aspecific epitope. From N-terminus to C-terminus, both light and heavychains comprise the domains FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4. Theassignment of amino acids to each domain is in accordance with thedefinitions of Kabat Sequences of Proteins of Immunological Interest(National Institutes of Health, Bethesda, Md. (1987 and 1991)).

The identity of the amino acid residues in a particular antibody thatmake up a CDR can be determined using methods well known in the art. Forexample, antibody CDRs may be identified as the hypervariable regionsoriginally defined by Kabat et al (Kabat et al., 1992, Sequences ofProteins of Immunological Interest, 5th ed., Public Health Service, NIH,Washington D.C.). The positions of the CDRs may also be identified asthe structural loop structures originally described by Chothia andothers (Chothia et al., 1989, Nature 342:877-883). Other approaches toCDR identification include the “AbM definition,” which is a compromisebetween Kabat and Chothia and is derived using Oxford Molecular's AbMantibody modeling software (now Accelrys®), or the “contact definition”of CDRs based on observed antigen contacts, set forth in MacCallum etal., 1996, J. Mol. Biol., 262:732-745. In another approach, referred toherein as the “conformational definition” of CDRs, the positions of theCDRs may be identified as the residues that make enthalpic contributionsto antigen binding (Makabe et al., 2008, Journal of BiologicalChemistry, 283:1156-1166). Still other CDR boundary definitions may notstrictly follow one of the above approaches, but will nonethelessoverlap with at least a portion of the Kabat CDRs, although they may beshortened or lengthened in light of prediction or experimental findingsthat particular residues or groups of residues or even entire CDRs donot significantly impact antigen binding. As used herein, a CDR mayrefer to CDRs defined by any approach known in the art, includingcombinations of approaches. The methods used herein may utilize CDRsdefined according to any of these approaches. For any given embodimentcontaining more than one CDR, the CDRs (or other residue of theantibody) may be defined in accordance with any of Kabat, Chothia,extended, AbM, contact, and/or conformational definitions.

The numbering of residues of the CLκ and CLλ domains can vary. Forexample, the numbering of the CLκ can begin at either LC-R¹⁰⁸ accordingto Kabat numbering (for example, R¹⁰⁸ of SEQ ID NO:2), or LC-T¹⁰⁹according to Kabat numbering (for example, T¹⁰⁹ of SEQ ID NO:2). Thenumbering convention used herein is that provided by the Swiss-Protgroup, a part of the Swiss Institute of Bioinformatics, and begins atLC-T¹⁰⁹. It will be appreciated that where a different numbering systemis preferred, the numbering of specified residues of the invention maybe adjusted accordingly. LC refers to Light Chain.

An “antibody” refers to an intact Ig or to an antigen binding portionthereof that competes with the intact antibody for specific binding.Antigen-binding portions may be produced by recombinant DNA techniquesor by enzymatic or chemical cleavage of intact antibodies.Antigen-binding portions include, inter alia, Fab, Fab′, F(ab′)2, Fv,dAb, and complementarity determining region (CDR) fragments,single-chain antibodies (scFv), chimeric antibodies, diabodies andpolypeptides that contain at least a portion of an Ig that is sufficientto confer specific antigen binding to the polypeptide. A Fab fragment isa monovalent fragment consisting of the VL, VH, CL and CH I domains; aF(ab′)2 fragment is a bivalent fragment comprising two Fab fragmentslinked by a disulfide bridge at the hinge region; a Fd fragment consistsof the VH and CH1 domains; an Fv fragment consists of the VL and VHdomains of a single arm of an antibody; and a dAb fragment consists of aVH domain or a VL domain (e.g. human, camelid, or shark).

In general, references to antibodies are to be construed as alsoreferring to antigen binding portions thereof, and in particular, mayinclude antigen binding portions thereof that comprise SEQ ID NO:98between their E and F β-strands .

A single-chain antibody (scFv) is an antibody in which a VL and VHregions are paired to form a monovalent molecules via a synthetic linkerthat enables them to be made as a single protein chain. Diabodies arebivalent, bispecific antibodies in which VH and VL domains are expressedon a single polypeptide chain, but using a linker that is too short toallow for pairing between the 2 domains on the same chain, therebyforcing the domains to pair with complementary domains of another chainand creating 2 antigen binding sites. One or more CDRs may beincorporated into a molecule either covalently or noncovalently to makeit an immunoadhesin. An immunoadhesin may incorporate the CDR (s) aspart of a larger polypeptide chain, may covalently link the CDR (s) toanother polypeptide chain, or may incorporate the CDR(s) noncovalently.The CDRs permit the immunoadhesin to specifically bind to a particularantigen of interest.

Mammalian light chains are of two types, κ and λ, and in any givenantibody molecule only one type occurs. Approximately twice as many κ asλ molecules are produced in humans but in other mammals this ratio canvary. Each free light chain molecule contains approximately 220 aminoacids in a single polypeptide chain that is folded to form the constantand variable region domains.

During B cell development, a recombination event at the DNA level joinsa single variable (V) segment with a joining (J) segment; the constant(C) segment is later joined by splicing at the RNA level. Recombinationof many different V segments with several J segments provides a widerange of antigen recognition. Additional diversity is attained byjunctional diversity, resulting from the random additional ofnucleotides by terminal deoxynucleotidyltransferase, and by somatichypermutation, which occurs during B cell maturation in the spleen andlymph nodes. Constant kappa (CLκ) regions are encoded by a single gene,whereas lambda constant (CLλ) regions are encoded by multiple genes, andundergo splicing. Several markers associated with particular polymorphicspecies of CLλ are known: IgCLλ1 (Mcg marker); IGLC2-IgCLλ2 (Kern-Oz−marker); IgCLλ 3 (Kern-Oz+ marker), and IgCLλ7, for example. The skilledperson can easily establish all of the polymorphisms so far identifiedin human CLλ chains. SEQ ID NO:93 incorporates many of the presentlyidentified polymorphisms. The sequences of the present inventionencompass other known polymorphisms of the CLκ and CLλ, and antibodiesin general. Two polymorphic loci have been identified in the CLκ;CLκ-V/A⁴⁵ and CLκ-L/V⁸³. The three polymorphisms so far identified are:Km(1): CLκ-V⁴⁵/L⁸³; Km(1,2): CLκ-A⁴⁵/L⁸³; and Km(3): CLκ-A⁴⁵/V⁸³.

An antibody may have one or more binding sites. If there is more thanone binding site, the binding sites may be identical to one another ormay be different. For instance, a naturally-occurring Ig has 2 identicalbinding sites, a single-chain antibody or Fab fragment has one bindingsite, while a “bispecific” or “bifunctional” antibody has 2 differentbinding sites.

An “isolated antibody” is an antibody that (1) is not associated withnaturally-associated components, including other naturally-associatedantibodies, that accompany it in its native state, (2) is free of otherproteins from the same species, (3) is expressed by a cell that does notnaturally express the antibody, or is expressed by a cell from adifferent species, or (4) does not occur in nature.

The term “human antibody” includes all antibodies that have one or morevariable and constant regions derived from human Ig sequences. In someembodiments of the present invention, all of the variable and constantdomains of the anti-IGF1R antibody are derived from human Ig sequences(a fully human antibody). A humanized antibody is an antibody that isderived from a non-human species, in which certain amino acids in theframework and constant domains of the heavy and light chains have beenmutated so as to avoid or abrogate an immune response in humans.Alternatively, a humanized antibody may be produced by fusing theconstant domains from a human antibody to the variable domains of anon-human species.

The term “chimeric antibody” refers to an antibody that contains one ormore regions from one antibody and one or more regions from one or moreother antibodies.

The term “epitope” includes any protein determinant capable of specificbinding to an Ig or T-cell receptor. Epitopic determinants usuallyconsist of chemically active surface groupings of molecules such asamino acids or sugar side chains and usually have specific 3 dimensionalstructural characteristics, as well as specific charge characteristics.An antibody is said to specifically bind an antigen when thedissociation constant is <1 uM, preferably <100 nM and more preferably:<10 nM.

The term multifunctional antibody conjugate, or MAC, refers to anantibody as defined herein, or antigen binding portion thereof,covalently conjugated to at least one Effector Moiety that binds to atarget. The Effector Moiety may be a peptide, small molecule, protein,nucleic acid molecule, toxin, aptamer, or antigen binding antibody orfragment thereof. References to conjugation of peptides and the likereferred to throughout the specification generally applies toconjugation to proteins and (antigen binding) antibodies or fragmentsthereof.

Fully human antibodies are expected to minimize the immunogenic andallergic responses intrinsic to mouse or mouse-derivatized monoclonalantibodies (Mabs) and thus to increase the efficacy and safety of theadministered antibodies. The use of fully human antibodies can beexpected to provide a substantial advantage in the treatment of chronicand recurring human diseases, such as inflammation and cancer, which mayrequire repeated antibody administrations. In another embodiment, theinvention provides a MAC comprising an antibody that does not bindcomplement.

In addition, fusion antibodies can be created in which 2 (or more)single-chain antibodies are linked to one another. This is useful if onewants to create a divalent or polyvalent antibody on a singlepolypeptide chain, or if one wants to create a bispecific antibody.

One type of derivatized antibody is produced by crosslinking 2 or moreantibodies (of the same type or of different types; e.g. to createbispecific antibodies). Suitable crosslinkers include those that areheterobifunctional, having 2 distinctly reactive groups separated by anappropriate spacer (e.g., m-maleimidobenzoyl-N-hydroxysuccinimide ester)or homobifunctional (e.g. disuccinimidyl suberate).

Another type of derivatized antibody is a labelled antibody. Usefuldetection agents with which an antibody or antibody portion of theinvention may be derivatized include fluorescent compounds, includingfluorescein, fluorescein isothiocyanate, rhodamine,5-dimethylamine-1-napthalenesulfonyl chloride, phycoerythrin, lanthanidephosphors and the like. An antibody may also be labelled with enzymesthat are useful for detection, such as horseradish peroxidase,galactosidase, luciferase, alkaline phosphatase, glucose oxidase and thelike. When an antibody is labelled with a detectable enzyme, it isdetected by adding additional reagents that the enzyme uses to produce areaction product that can be discerned. For example, when the agenthorseradish peroxidase is present, the addition of hydrogen peroxide anddiaminobenzidine leads to a colored reaction product, which isdetectable. An antibody may also be labelled with biotin, and detectedthrough indirect measurement of avidin or streptavidin binding. Anantibody may be labelled with a magnetic agent, such as gadolinium. Anantibody may also be labelled with a predetermined polypeptide epitoperecognized by a secondary reporter (e.g. leucine zipper pair sequences,binding sites for secondary antibodies, metal binding domains, epitopetags). In some embodiments, labels are attached by spacer arms ofvarious lengths to reduce potential steric hindrance.

The antibody may also be derivatized with a chemical group such aspolyethylene glycol (PEG), a methyl or ethyl group, or a carbohydrategroup. These groups may be useful to improve the biologicalcharacteristics of the antibody, e.g. to increase serum half-life or toincrease tissue binding.

Antibody Specificity

In some embodiments comprising antigen binding domains, the antigenbinding domain (for example, but not limited to, an antibody variableregion having all 6 CDRs, or an equivalent region that is at least 90percent identical to an antibody variable region) is chosen from:abagovomab, abatacept (ORENCIA®), abciximab (REOPRO®, c7E3 Fab),adalimumab (HUMIRA®), adecatumumab, alemtuzumab (CAMPATH®, MabCampath orCampath-1H), altumomab, afelimomab, anatumomab mafenatox, anetumumab,anrukizumab, apolizumab, arcitumomab, aselizumab, atlizumabi,atorolimumab, bapineuzumab, basiliximab (SIMULECT®), bavituximab,bectumomab (LYMPHOSCAN®), belimumab (LYMPHO-STAT-B®), bertilimumab,besilesomab, βcept (ENBREL®), bevacizumab (AVASTIN®), biciromabbrallobarbital, bivatuzumab mertansine, brentuximab vedotin (ADCETRIS®),canakinumab (ACZ885), cantuzumab mertansine, capromab (PROSTASCINT®),catumaxomab (REMOV AB®)), cedelizumab (CIMZIA®), certolizumab pegol,cetuximab (ERBITUX®), clenoliximab, dacetuzumab, dacliximab, daclizumab(ZENAP AX®), denosumab (AMG 162), detumomab, dorlimomab aritox,dorlixizumab, duntumumab, durimulumab, durmulumab, ecromeximab,eculizumab (SOLIRIS®), edobacomab, edrecolomab (Mabl7-1A, PANOREX®),efalizumab (RAPTIVA®), efungumab (MYCOGRAB®), elsilimomab, enlimomabpegol, epitumomab cituxetan, efalizumab, epitumomab, epratuzumab,erlizumab, ertumaxomab (REXOMUN®), etaracizumab (etaratuzumab, VITAXIN®,ABEGRIN™), exbivirumab, fanolesomab (NEUTROSPEC®), faralimomab,felvizumab, fontolizumab (HUZAF®), galiximab, gantenerumab, gavilimomab(ABX-CBL®), gemtuzumab ozogamicin (MYLOTARG®), golimumab (CNTO 148),gomiliximab, ibalizumab (TNX-355), ibritumomab tiuxetan (ZEVALIN®),igovomab, imciromab, infliximab (REMICAD E®)), inolimomab, inotuzumabozogamicin, ipilimumab (YERVOY®, MDX-010), iratumumab, keliximab,labetuzumab, lemalesomab, lebrilizumab, lerdelimumab, lexatumumab(HGS-ETR2, ETR2-ST01), lexitumumab, libivirumab, lintuzumab,lucatumumab, lumiliximab, mapatumumab (HGS-ETRI, TRM-I), maslimomab,matuzumab (EMD72000), mepolizumab (BOSATRIA®), metelimumab, milatuzumab,minretumomab, mitumomab, morolimumab, motavizumab (NUMAX™), muromonab(OKT3), nacolomab tafenatox, naptumomab estafenatox, natalizumab(TYSABRI®, ANTEGREN®), nebacumab, nerelimomab, nimotuzumab (THERACIMhR3®, THERA-CIM-hR3®, THERALOC®), nofetumomab merpentan (VERLUMA®),ocrelizumab, odulimomab, ofatumumab, omalizumab (XOLAIR®), oregovomab(OVAREX®), otelixizumab, pagibaximab, palivizumab (SYNAGIS®),panitumumab (ABX-EGF, VECTIBIX®), pascolizumab, pemtumomab (THERAGYN®),pertuzumab (2C4, OMNITARG®), pexelizumab, pintumomab, ponezumab,priliximab, pritumumab, ranibizumab (LUCENTIS®), raxibacumab,regavirumab, reslizumab, rituximab (RITUXAN®, MabTHERA®), rovelizumab,ruplizumab, satumomab, sevirumab, sibrotuzumab, siplizumab (MEDI-507),sontuzumab, stamulumab (Myo-029), sulesomab (LEUKOSCAN®), tacatuzumabtetraxetan, tadocizumab, talizumab, taplitumomab paptox, tefibazumab(AUREXIS®), telimomab aritox, teneliximab, teplizumab, ticilimumab,tocilizumab (ACTEMRA®), toralizumab, tositumomab, trastuzumab(HERCEPTIN®), tremelimumab (CP-675,206), tucotuzumab celmoleukin,tuvirumab, urtoxazumab, ustekinumab (CNTO 1275), vapaliximab,veltuzumab, vepalimomab, visilizumab (NUVION®), volociximab (M200),votumumab (HUMASPECT®), zalutumumab, zanolimumab (HuMAX-CD4),ziralimumab, or zolimomab aritox.

In some embodiments comprising antigen binding domains, the antigenbinding domain comprise a heavy and light chain variable domain havingsix CDRs, and/or compete for binding with an antibody selected from thepreceding list. In some embodiments comprising antigen binding domains,the antigen binding domain binds the same epitope as the antibodies inthe preceding list. In some embodiments comprising antigen bindingdomains, the antigen binding domain comprises a heavy and light chainvariable domain having six total CDRs, and binds to the same antigen asthe antibodies in the preceding list.

In some embodiments comprising antigen binding domains, the antigenbinding domain comprises a heavy and light chain variable domain havingsix (6) total CDRs, and specifically binds to an antigen selected from:PDGFRα, PDGFRβ, PDGF, VEGF, VEGF-A, VEGF-B, VEGF-C, VEGF-D, VEGF-E,VEGF-F, VEGFR1, VEGFR2, VEGFR3, FGF, FGF2, HGF, KDR, flt-1, FLK-1,Ang-2, Ang-1, PLGF, CEA, CXCL13, Baff, IL-21, CCL21, TNF-α, CXCL12,SDF-I, bFGF, MAC-I, IL23pl9, FPR, IGFBP4, CXCR3, TLR4, CXCR2, EphA2,EphA4, EphrinB2, EGFR (ErbBI), HER2 (ErbB2 or pl85neu), HER3 (ErbB3),HER4ErbB4 or tyro2), SCI, LRP5, LRP6, RAGE, s100A8, s100A9, Navl.7,GLPI, RSV, RSV F protein, Influenza HA protein, Influenza NA protein,HMGBI, CD16, CD19, CD20, CD21, CD28, CD32, CD32b, CD64, CD79, CD22,ICAM-I, FGFRI, FGFR2, HDGF, EphB4, GITR, β-amyloid, hMPV, PIV-I, PIV-2,OX40L, IGFBP3, cMet, PD-I, PLGF, Neprolysin, CTD, IL-18, IL-6, CXCL-13,IL-IRI, IL-15, IL-4R, IgE, PAI-I, NGF, EphA2, uPARt, DLL-4, αvβ35, αvβ6,α5β1, α3β1, interferon receptor type I and type II, CD 19, ICOS, IL-17,Factor II, Hsp90, IGF, IGF-I, IGF-II, CD 19, GM-CSFR, PIV-3, CMV, IL-13,IL-9, and EBV.

In some embodiments comprising antigen binding domains, the antigenbinding domain specifically binds to a member (receptor or ligand) ofthe TNF superfamily. Various molecules include, but are not limited toTumor Necrosis Factor-α (“TNF-α”), Tumor Necrosis Factor-β (“TNF-β”),Lymphotoxin-α (“LT-α”), CD30 ligand, CD27 ligand, CD40 ligand, 4-1 BBligand, Apo-1 ligand (also referred to as Fas ligand or CD95 ligand),Apo-2 ligand (also referred to as TRAIL), Apo-3 ligand (also referred toas TWEAK), osteoprotegerin (OPG), APRIL, RANK ligand (also referred toas TRANCE), TALL-I (also referred to as BlyS, BAFF or THANK), DR4, DR5(also known as Apo-2, TRAIL-R2, TR6, Tango-63, hAPO8, TRICK2, orKILLER), DR6, DcRI, DcR2, DcR3 (also known as TR6 or M68), CARI, HVEM(also known as ATAR or TR2), GITR, ZTNFR-5, NTR-I, TNFLI, CD30, LTBr,4-1 BB receptor and TR9.

In some embodiments comprising antigen binding domains, the antigenbinding domain is capable of binding one or more targets chosen from5T4, ABL, ABCB5, ABCFI, ACVRI, ACVRIB, ACVR2, ACVR2B, ACVRLI, AD0RA2A,Aggrecan, AGR2, AICDA, AIFI, AIGI, AKAPI, AKAP2, AMH, AMHR2, angiogenin(ANG), ANGPTI, ANGPT2, ANGPTL3, ANGPTL4, Annexin A2, ANPEP, APC, APOCI,AR, aromatase, ATX, AXI, AZGPI (zinc-a-glycoprotein), B7.1, B7.2, B7-H1,BAD, BAFF, BAGI, BAII, BCR, BCL2, BCL6, BDNF, BLNK, BLRI (MDR15), BlyS,BMP1, BMP2, BMP3B (GDFIO), BMP4, BMP6, BMP7, BMP8, BMP9, BMP11, BMP12,BMPR1A, BMPR1B, BMPR2, BPAGI (plectin), BRCAI, C19orflO (IL27w), C3,C4A, C5, C5R1, CANTI, CASPI, CASP4, CAVI, CCBP2 (D6/JAB61), CCLI(1-309), CCLI 1 (eotaxin), CCL13 (MCP-4), CCL15 (MIP-Id), CCL16 (HCC-4),CCL17 (TARC), CCL18 (PARC), CCL19 (MIP-3b), CCL2 (MCP-1), MCAF, CCL20(MIP-3a), CCL21 (MEP-2), SLC, exodus-2, CCL22 (MDC/STC-I), CCL23(MPIF-I), CCL24 (MPIF-2/eotaxin-2), CCL25 (TECK), CCL26 (eotaxin-3),CCL27 (CTACK/ILC), CCL28, CCL3 (MIP-Ia), CCL4 (MIP-Ib), CCL5 (RANTES),CCL7 (MCP-3), CCL8 (mcp-2), CCNAI, CCNA2, CCNAI, CCNEI, CCNE2, CCRI(CKRI/HM145), CCR2 (mcp-IRB/RA), CCR3 (CKR3/CMKBR3), CCR4, CCR5(CMKBR5/ChemR13), CCR6 (CMKBR6/CKR-L3/STRL22/DRY6), CCR7 (CKR7/EBI1),CCR8 (CMKBR8/TERI/CKR-LI), CCR9 (GPR-9-6), CCRLI (VSHKI), CCRL2 (L-CCR),CD164, CD19, CDIC, CD20, CD200, CD-22, CD24, CD28, CD3, CD33, CD35,CD37, CD38, CD3E, CD3G, CD3Z, CD4, CD40, CD40L, CD44, CD45RB, CD46,CD52, CD69, CD72, CD74, CD79A, CD79B, CD8, CD80, CD81, CD83, CD86,CD105, CD137, CDHI (E-cadherin), CDCP1CDH10, CDH12, CDH13, CDH18, CDH19,CDH20, CDH5, CDH7, CDH8, CDH9, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK9,CDKNIA (p21Wapl/Cipl), CDKNIB (p27Kipl), CDKNIC, CDKN2A (pl6INK4a),CDKN2B, CDKN2C, CDKN3, CEBPB, CERI, CHGA, CHGB, Chitinase, CHSTIO,CKLFSF2, CKLFSF3, CKLFSF4, CKLFSF5, CKLFSF6, CKLFSF7, CKLFSF8, CLDN3,CLDN7 (claudin-7), CLN3, CLU (clusterin), CMKLRI, CMKORI (RDCI), CNRI,COLI 8AI, COL1A1.COL4A3, COL6A1, CR2, Cripto, CRP, CSFI (M-CSF), CSF2(GM-CSF), CSF3 (GCSF), CTLA4, CTL8, CTNNBI (b-catenin), CTSB (cathepsinB), CX3CL1 (SCYDI), CX3CR1 (V28), CXCLI (GROI), CXCLIO (IP-IO), CXCLII(I-TAC/IP-9), CXCL12 (SDFI), CXCL13, CXCL 14, CXCL 16, CXCL2 (GR02),CXCL3 (GR03), CXCL5 (ENA-78/LIX), CXCL6 (GCP-2), CXCL9 (MIG), CXCR3(GPR9/CKR-L2), CXCR4, CXCR6 (TYMSTR/STRL33/Bonzo), CYB5, CYCI, Cyr61,CYSLTRI, c-Met, DAB2IP, DES, DKFZp451J0118, DNCLI, DPP4, E2F1,ECGFI5EDGI, EFNAI, EFNA3, EFNB2, EGF, ELAC2, ENG, endoglin, ENOI, EN02,EN03, EPHAI, EPHA2, EPHA3, EPHA4, EPHA5, EPHA6, EPHA7, EPHA8, EPHA9,EPHAIO, EPHBI, EPHB2, EPHB3, EPHB4, EPHB5, EPHB6, EPHRIN-A1, EPHRIN-A2,EPHRIN-A3, EPHRIN-A4, EPHRIN-A5, EPHRIN-A6, EPHRIN-BI, EPHRIN-B2,EPHRTN-B3, EPHB4, EPG, ERBB2 (Her-2), EREG, ERK8, Estrogen receptor,ESRI, ESR2, F3 (TF), FADD, farnesyltransferase, FasL, FASNf, FCER1A,FCER2, FCGR3A, FGF, FGFI (aFGF), FGFIO, FGFI 1, FGF12, FGF12B, FGF13,FGF14, FGF16, FGF17, FGF18, FGF19, FGF2 (bFGF), FGF20, FGF21 (such asmimAb1), FGF22, FGF23, FGF3 (int-2), FGF4 (HST), FGF5, FGF6 (HST-2),FGF7 (KGF), FGF8, FGF9, FGFR3, FIGF (VEGFD), FILI (EPSILON), FBLI(ZETA), FLJ12584, FLJ25530, FLRTI (fibronectin), FLTI, FLT-3, FOS, FOSLI(FRA-I), FY (DARC), GABRP (GABAa), GAGEBI, GAGECI, GALNAC4S-6ST, GATA3,GD2, GD3, GDF5, GDF8, GFII, GGTI, GM-CSF, GNASI, GNRHI, GPR2 (CCRIO),GPR31, GPR44, GPR81 (FKSG80), GRCCIO (CIO), gremlin, GRP, GSN(Gelsolin), GSTPI, HAVCR2, HDAC, HDAC4, HDAC5, HDAC7A, HDAC9, Hedgehog,HGF, HIFIA, HIPI, histamine and histamine receptors, HLA-A, HLA-DRA,HM74, HMOXI, HSP90, HUMCYT2A, ICEBERG, ICOSL, ID2, IFN-a, IFNAI, IFNA2,IFNA4, IFNA5, EFNA6, BFNA7, IFNBI, IFNgamma, IFNWI, IGBPI, IGFI, IGFIR,IGF2, IGFBP2, IGFBP3, IGFBP6, DL-I, ILIO, ILIORA, ILIORB, IL-1, ILIRI(CD121a), ILIR2 (CD121b), IL-IRA, IL-2, IL2RA (CD25), IL2RB (CD122),IL2RG (CD132), IL-4, IL-4R (CD123), IL-5, IL5RA (CD125), IL3RB (CD131),IL-6, IL6RA (CD126), IR6RB (CD130), IL-7, IL7RA (CD127), IL-8, CXCRI(IL8RA), CXCR2 (IL8RB/CD128), IL-9, IL9R (CD129), IL-10, IL10RA (CD210),IL10RB (CDW210B), IL-11, ILI IRA, IL-12, IL-12A, IL-12B, IL-12RB1,IL-12RB2, IL-13, IL13RA1, IL13RA2, IL14, IL15, IL15RA, IL16, IL17,IL17A, IL17B, IL17C, IL17R, IL18, IL18BP, IL18RI, IL18RAP, IL19, ILIA,ILIB, ILIFIO, IL1F5, IL1F6, IL1F7, IL1F8, DL1F9, ILIHYI, ILIRI, IL1R2,ILIRAP, ILIRAPLI, IL1RAPL2, ILIRLI, IL1RL2, ILIRN, IL2, IL20, IL20RA,IL21R, IL22, IL22R, IL22RA2, IL23, DL24, IL25, IL26, IL27, IL28A, IL28B,IL29, IL2RA, IL2RB, IL2RG, IL3, IL30, IL3RA, IL4, IL4R, IL6ST(glycoprotein 130), ILK, INHA, INHBA, INSL3, INSL4, IRAKI, IRAK2, ITGA1,ITGA2, ITGA3, ITGA6 (α 6 integrin), ITGAV, ITGB3, ITGB4 (β 4 integrin),JAKI, JAK3, JTB, JUN, K6HF, KAII, KDR, KIM-1, KITLG, KLF5 (GC Box BP),KLF6, KLKIO, KLK12, KLK13, KLK14, KLK15, KLK3, KLK4, KLK5, KLK6, KLK9,KRTI, KRT19 (Keratin 19), KRT2A, KRTHB6 (hair-specific type II keratin),LAMAS, LEP (leptin), Lingo-p75, Lingo-Troy, LPS, LRP5, LRP6, LTA(TNF-b), LTB, LTB4R (GPR16), LTB4R2, LTBR, MACMARCKS, MAG or Omgp,MAP2K7 (c-Jun), MCP-I, MDK, MIBI, midkine, MIF, MISRII, MJP-2, MK, MKI67(Ki-67), MMP2, MMP9, MS4A1, MSMB, MT3 (metallothionectin-Ui), mTOR,MTSSI, MUCI (mucin), MYC, MYD88, NCK2, neurocan, neuregulin-1,neuropilin-1, NFKBI, NFKB2, NGFB (NGF), NGFR, NgR-Lingo, NgR-Nogo66(Nogo), NgR-p75, NgR-Troy, NMEI (NM23A), NOTCH, NOTCHI, N0X5, NPPB,NROBI, NR0B2, NRIDI, NR1D2, NR1H2, NR1H3, NR1H4, NR1I2, NR1I3, NR2C1,NR2C2, NR2E1, NR2E3, NR2F1, NR2F2, NR2F6, NR3C1, NR3C2, NR4A1, NR4A2,NR4A3, NR5A1, NR5A2, NR6A1, NRPI, NRP2, NT5E, NTN4, OCT-1, ODZ1, OPN1,OPN2, OPRDI, P2RX7, PAP, PARTI, PATE, PAWR, PCA3, PCDGF, PCNA, PDGFA,PDGFB, PDGFRA, PDGFRB, PECAMI, peg-asparaginase, PF4 (CXCL4), Plexin B2(PLXNB2), PGF, PGR, phosphacan, PIAS2, PI3 Kinase, PIK3CG, PLAU (uPA),PLG5PLXDCI, PKC, PKC-β, PPBP (CXCL7), PPID, PRI, PRKCQ, PRKDI, PRL,PROC, PROK2, pro-NGF, prosaposin, PSAP, PSCA, PTAFR, PTEN, PTGS2(COX-2), PTN, RAC2 (P21Rac2), RANK, RANK ligand, RARB, RGSI, RGS13,RGS3, RNFI10 (ZNF144), Ron, R0B02, RXR, selectin, S100A2, S100A8,S100A9, SCGB 1D2 (lipophilin B), SCGB2A1 (mammaglobin 2), SCGB2A2(mammaglobin 1), SCYEI (endothelial Monocyte-activating cytokine), SDF2,SERPENA1, SERPINA3, SERPINB5 (maspin), SERPINEI (PAI-I), SERPINFI,SHIP-I, SHIP-2, SHBI, SHB2, SHBG, SfcAZ, SLC2A2, SLC33A1, SLC43A1,SLIT2, SPPI, SPRRIB (Sprl), ST6GAL1, STABI, STATE, STEAP, STEAP2,SULF-1, Sulf-2, TB4R2, TBX21, TCPIO, TDGFI, TEK, TGFA, TGFBI, TGFBIII,TGFB2, TGFB3, TGFBI, TGFBRI, TGFBR2, TGFBR3, THIL, THBSI(thrombospondin-1), THBS2/THBS4, THPO, TIE (Tie-1), TIMP3, tissuefactor, TIKI2, TLR10, TLR2, TLR3, TLR4, TLR5, TLR6JLR7, TLR8, TLR9,TM4SF1, TNF, TNF-a, TNFAIP2 (B94), TNFAIP3, TNFRSFIIA, TNFRSFIA,TNFRSFIB, TNFRSF21, TNFRSF5, TNFRSF6 (Fas), TNFRSF7, TNFRSF8, TNFRSF9,TNFSFIO (TRAIL), TNFSFI 1 (TRANCE), TNFSF12 (AP03L), TNFSF13 (April),TNFSF13B, TNFSF14 (HVEM-L), TNFSF15 (VEGI), TNFSF 18, TNFSF4 (0×40ligand), TNFSF5 (CD40 ligand), TNFSF6 (FasL), TNFSF7 (CD27 ligand),TNFSF8 (CD30 ligand), TNFSF9 (4-1 BB ligand), TOLLIP, Toll-likereceptors, TLR2, TLR4, TLR9, TP02A (topoisomerase Iia), TP53, TPMI,TPM2, TRADD, TRAFI, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6, TRKA, TREMI,TREM2, TRPC6, TROY, TSLP, TWEAK, Tyrosinase, uPAR, VEGF, VEGFB, VEGFC,versican, VHL C5, VLA-4, Wnt-1, XCLI (lymphotactin), XCL2 (SCM-Ib), XCRI(GPR5/CCXCRI), YYI, and ZFPM2.

Catalytic Antibodies

In some aspects of the invention, the MAC comprises a catalyticantibody, or antigen binding portion thereof. In some aspects, theantibody may be an aldolase antibody.

The contents of US2006205670 are incorporated herein by reference—inparticular paragraphs [0153]-[0233], describing antibodies, usefulfragments and variants and modifications thereof, combining sites andCDRs, antibody preparation, expression, humanization, amino acidmodification, glycosylation, ADCC, CDC, increasing serum half life ofantibodies, expression vectors, mammalian host systems, and folding,amongst other elements of antibody technology.

“Combining site”, as used herein, (also known as the antibody bindingsite) refers to the region of the Ig or Ig domains that combine (or cancombine) with the determinant of an appropriate antigen (or astructurally similar protein). The term generally includes the CDRs andthe adjacent framework residues that are involved in antigen binding.

“Aldolase antibodies” as used herein, refers to antibodies containingcombining site portions that, when unencumbered (for example byconjugation), catalyze an aldol addition reaction between an aliphaticketone donor and an aldehyde acceptor. Aldolase antibodies are capableof being generated by immunization of an immune-responsive animal withan immunogen that includes a 1,3 diketone hapten of the formula:

coupled to a carrier protein, and further characterized by having alysine with a reactive ε-amino group in the combining site of theantibody. Aldolase antibodies are further characterized by theircatalytic activity being subject to inhibition with the 1,3-diketonehapten by formation of a complex between the 1,3-diketone hapten and theε-amino group of the lysine of the catalytic antibody.

As discussed, in certain embodiments, certain antibodies that can beused to make MACs, compositions and samples of the invention maycomprise a reactive side chain in the antibody combining site. Areactive side chain may be present naturally or may be placed in anantibody by mutation. The reactive residue of the antibody combiningsite may be associated with the antibody, such as when the residue isencoded by nucleic acid present in the lymphoid cell first identified tomake the antibody. Alternatively, the amino acid residue may arise bypurposely mutating the DNA so as to encode the particular residue. Thereactive residue may be a non-natural residue arising, for example, bybiosynthetic incorporation using a unique codon, tRNA, andaminoacyl-tRNA as discussed herein. In another approach, the amino acidresidue or its reactive functional groups (e.g., a nucleophilic aminogroup or sulfhydryl group) may be attached to an amino acid residue inthe antibody combining site. Thus, covalent linkage with the antibodyoccurring “through an amino acid residue in a combining site of anantibody” as used herein means that linkage can be directly to an aminoacid residue of an antibody combining site or through a chemical moietythat is linked to a side chain of an amino acid residue of an antibodycombining site. In some embodiments, the amino acid is cysteine, and thereactive group of the side chain is a sulfhydryl group. In otherembodiments, the amino acid residue is lysine, and the reactive group ofthe side chain is the ε-amino group. In some embodiments, the amino acidis K⁹³ on the heavy chain according to Kabat numbering. In someembodiments, the amino acid is on HC-K⁹⁹ of h38C2 according to thenumbering of SEQ ID NOs: 65 and 66.

Catalytic antibodies are one source of antibodies with suitablecombining sites that comprise one or more reactive amino acid sidechains. Such antibodies include aldolase antibodies, β lactamaseantibodies, esterase antibodies, and amidase antibodies.

One embodiment comprises an aldolase antibody such as the mousemonoclonal antibodies mAb 33F12 and mAb 38C2 (whose VL and VH compriseSEQ ID NO:68 and 69), as well as suitably chimeric and humanizedversions of such antibodies (e.g. h38C2IgG1: SEQ ID NOs:64 and 65 andh38C2-IgG2: SEQ ID NOs:64 and 66). In favourable aspects, a heavy chainsuch as SEQ ID NO:65 or SEQ ID NO:66 is used in conjunction with theh38C2 VL (SEQ ID NO:67) fused to one of the CL domains of the inventioncomprising SEQ ID NO:98.

Mouse mAb 38C2 (and h38C2) has a reactive lysine near to but outsideHCDR3, and is the prototype of a new class of catalytic antibodies thatwere generated by reactive immunization and mechanistically mimicnatural aldolase enzymes. Other aldolase catalytic antibodies that maybe used include the antibodies produced by the hybridoma 85A2, havingATCC accession number PTA-1015; hybridoma 85C7, having ATCC accessionnumber PTA-1014; hybridoma 92F9, having ATCC accession number PTA-1017;hybridoma 93F3, having ATCC accession number PTA-823; hybridoma 84G3,having ATCC accession number PTA-824; hybridoma 84G11, having ATCCaccession number PTA-1018; hybridoma 84H9, having ATCC accession numberPTA-1019; hybridoma 85H6, having ATCC accession number PTA-825;hybridoma 90G8, having ATCC accession number PTA-1016. Through areactive lysine, these antibodies catalyze aldol and retro-aldolreactions using the enamine mechanism of natural aldolases.

Compounds of the invention may also be formed by linking a targetingagent to a reactive cysteine, such as those found in the combining sitesof thioesterase and esterase catalytic antibodies. Reactive aminoacid-containing antibodies may be prepared by means well known in theart, including mutating an antibody combining site residue to encode forthe reactive amino acid or chemically derivatizing an amino acid sidechain in an antibody combining site with a linker that contains thereactive group.

The antibody may be a humanized antibody. Where compounds of theinvention are covalently linked to the combining site of an antibody,and such antibodies are humanized, it is important that such antibodiesbe humanized with retention of high linking affinity for the W group.Various forms of humanized murine aldolase antibodies are contemplated.One embodiment uses the humanized aldolase catalytic antibody h38c2 IgG1or h38c2 Fab with human constant domains CLκ and CHγ₁1. Human germlineVLk gene DPK-9 and human Jk gene JK4 were used as frameworks for thehumanization of the kappa light chain variable domain of m38c2, andhuman germline gene DP-47 and human JH gene JH4 were used as frameworksfor the humanization of the heavy chain variable domain of m38c2. FIG.8A illustrates a sequence alignment between the variable light and heavychains in m38c2, h38c2, and human germlines. h38c2 may utilize IgG1,IgG2, IgG3, or IgG4 constant domains, including any of the allotypesthereof. Another embodiment uses a chimeric antibody comprising thevariable domains (VL and VH) of h38c2 (SEQ ID NOs: 67 and 68) and theconstant domains from an IgG1, IgG2, IgG3, or IgG4 antibody thatcomprises a polypeptide of the invention comprising SEQ ID NO:98 betweenβ-sheets E and F. The LC may comprise SEQ ID NO:254. The antibody may bea full-length antibody, Fab, Fab′, F(ab′)₂, VH, VL, diabody, or minibodycomprising VH and VL domains from h38c2. The antibody may be an antibodycomprising the VL and VH domains from h38c2 and a constant domainselected from the group consisting of IgG1, IgG2, IgG3, and IgG4. Theantibody may be a humanized version of a murine aldolase antibodycomprising a constant region from a human IgG, IgA, IgM, IgD, or IgEantibody. In another embodiment, the antibody is a chimeric antibodycomprising the VL and VH region from a murine aldolase antibody (e.g.SEQ ID NO:69 and 70) and a constant region from a human IgG, IgA, IgM,IgD, or IgE antibody, comprising a polypeptide of the inventioncomprising SEQ ID NO:98 between β-sheets E and F. In furtherembodiments, the antibody is a fully human version of a murine aldolaseantibody comprising a polypeptide sequence from natural or native humanIgG, IgA, IgM, IgD, or IgE antibody.

One embodiment uses h38c2 F(ab′)₂. h38c2 F(ab′)₂ may be produced by theproteolytic digestion of h38c2 IgG1.

As used herein, “pharmacokinetics” refers to the concentration of anadministered compound in the serum over time. Pharmacodynamics refers tothe concentration of an administered compound in target and nontargettissues over time and the effects on the target tissue (e.g., efficacy)and the non-target tissue (e.g., toxicity). Improvements in, forexample, pharmacokinetics or pharmacodynamics can be designed for aparticular targeting agent or biological agent, such as by using labilelinkages or by modifying the chemical nature of any linker (e.g.,changing solubility, charge, and the like). The term “K_(off)” refers tothe off rate constant for dissociation of an antibody from theantibody/antigen complex. The term“K_(d)” refers to the dissociationconstant of a particular antibody-antigen interaction.

In some aspects, the invention provides for pharmaceutically acceptablesalts, stereoisomers, tautomers, solvates, and prodrugs of compounds,samples, compositions and pharmaceutical compositions of the invention.

Catalytic Antibody Linkers

Certain linkers suitable for connecting targeting agents (TA) to thecombining site of catalytic antibodies (Catalytic Antibody Linkers:CAb-linkers) are disclosed in US2009098130, the contents of which areincorporated herein by reference. The term “targeting agents” is usedherein to distinguish from the term “Effector Moiety” but it is apparentthat the types of molecules attached at the end of a CAb-linker as a TA,or attached to the end of a MAC-linker as an Effector Moiety may beinterchangable. In particular, aspects of US2009098130 pertaining to thegeneral formulae describing (CAb-linkers, specific CAb-linker structure,synthesis of Cab-linkers and combinations of different elements of P¹,Q¹ and W¹, (therein classified as X, Y and Z groups respectively) asspecifically and generally described therein are herein included.

The CAb-linker may be linear or branched, and optionally includes one ormore carbocyclic or heterocyclic groups. CAb-linker length may be viewedin terms of the number of linear atoms, with cyclic moieties such asaromatic rings and the like to be counted by taking the shortest routearound the ring. In some embodiments, the CAb-linker has a linearstretch of between 5-15 atoms, in other embodiments 15-30 atoms, instill other embodiments 30-50 atoms, in still other embodiments 50-100atoms, and in still other embodiments 100-200 atoms. Other CAb-linkerconsiderations include the effect on physical or pharmacokineticproperties of the resulting compound, such as solubility, lipophilicity,hydrophilicity, hydrophobicity, stability (more or less stable as wellas planned degradation), rigidity, flexibility, immunogenicity, andmodulation of antibody binding, the ability to be incorporated into amicelle or liposome, and the like.

In some aspects the CAb-linker may be covalently linked to the sidechain of the TA-linking residue. The linker may comprise the formula:P¹-Q¹-W¹; wherein P¹ is a biologically compatible connecting chainincluding any atom selected from the group consisting of C, H, N, O, P,S, F, Cl, Br, and I, and may comprise a polymer or block co-polymer, andis covalently linked to the linking residue (through side chain, aminoterminus, or carboxyl terminus as appropriate) where the linker islinear, Q¹ is an optionally present recognition group comprising atleast a ring structure; and W¹ is an attachment moiety comprising acovalent link to an amino acid side chain in a combining site of anantibody.

When present, Q¹ may have the optionally substituted structure:

wherein a, b, c, d, and e are independently carbon or nitrogen; f iscarbon, nitrogen, oxygen, or sulfur; Q¹ is attached to P¹ and W¹independently at any 2 ring positions of sufficient valence; and no morethan 4 of a, b, c, d, e, or f are simultaneously nitrogen and preferablya, b, c, d, and e in the ring structure are each carbon. In someaspects, Q¹ may be phenyl. Although not wishing to be bound by anytheory, it is believed that the Q¹ group can assist in positioning thereactive group into a suitable antibody combining site so that the W¹group can react with a reactive amino acid side chain.

The CAb-linker may be designed such that it contains a reactive groupcapable of covalently or non-covalently forming a bond with amacromolecule, such as an antibody, protein, or fragment thereof. Thereactive group is chosen for use with a reactive residue in a particularcombining site. For example, a chemical moiety for modification by analdolase antibody may be a ketone, diketone, β lactam, active esterhaloketone, lactone, anhydride, maleimide, α-haloacetamide, cyclohexyldiketone, epoxide, aldehyde, amidine, guanidine, imine, enamine,phosphate, phosphonate, epoxide, aziridine, thioepoxide, masked orprotected diketone (ketal for example), lactam, haloketone, aldehyde,and the like.

In some embodiments, W¹, prior to conjugation with the side-chain of aresidue in the combining site of an antibody, includes one or more C═Ogroups arranged to form an azetidinone, diketone, an acyl β-lactam, anactive ester, a haloketone, a cyclohexyl diketone group, an aldehyde, amaleimide, an activated alkene, an activated alkyne or, in general, amolecule comprising a leaving group susceptible to nucleophilic orelectrophilic displacement. Other groups may include a lactone, ananhydride, an α-haloacetamide, an imine, a hydrazide, or an epoxide.Exemplary linker electrophilic reactive groups that can covalently bondto a reactive nucleophilic group (e.g., a lysine or cysteine side chain)in a combining site of antibody include acyl β-lactam, simple diketone,succinimide active ester, maleimide, haloacetamide with linker,haloketone, cyclohexyl diketone, aldehyde, amidine, guanidine, imine,enamine, phosphate, phosphonate, epoxide, aziridine, thioepoxide, amasked or protected diketone (a ketal, for example), lactam, sulfonate,and the like, masked C═O groups such as imines, ketals, acetals, and anyother known electrophilic group. In certain embodiments, the reactivegroup includes one or more C═O groups arranged to form an acyl β-lactam,simple diketone, succinimide active ester, maleimide, haloacetamide withlinker, haloketone, cyclohexyl diketone, or aldehyde. W¹ may be asubstituted alkyl, substituted cycloalkyl, substituted aryl, substitutedarylalkyl, substituted heterocyclyl, or substituted heterocyclylalkyl,wherein at least one substituent is a 1,3-diketone moiety, an acylβ-lactam, an active ester, an α-haloketone, an aldehyde, a maleimide, alactone, an anhydride, an α-haloacetamide, an amine, a hydrazide, or anepoxide. In some aspects, the W¹ group is covalently linked to amacromolecule scaffold that can provide increased half-life to thepeptides of the invention. In some aspects, the W¹ group if present iscovalently linked to the combining site of an antibody.

In some aspects, prior to conjugation (for example, with the combiningsite of an antibody), W¹ has the structure:

wherein q=0-5. q may be 1 or 2. q may be 1. In other aspects, q may be2.In some aspects, following conjugation with the antibody combining site,W¹ has the structure:

wherein q=0-5 and Antibody-N- is a covalent bond to a side chain in acombining site of an antibody. q may be 1 or 2. q may be 1. In otheraspects, q may be 2. P¹ may be a group comprising three components;P¹p-P¹s-P¹y, wherein P¹p is a group specifically adapted to becombinable with the targeting agent, P¹s is a spacer region of the P¹group, and P¹y is a group adapted to bind to the W¹ group. In someaspects, P¹y is selected from an amide bond, an enamine bond, or aguanidinium bond. P¹y may be selected so as to provide a hydrogenmolecule adjacent (within two atoms) to the Q¹ group. While not wishingto be bound by theory, it is believed that the H atom can assist the Q¹group recognition of a hydrophobic pocket through H-bond interaction,particularly in respect of the hydrophobic pocket of the binding cleftof a catalytic antibody, such as h38C2. Thus the amide bond, forexample, may be orientated such that the NH group is directly bonded tothe Q¹ group, providing the H of the NH group for hydrogen bonding.Alternatively, the C═O group of an amide may be bonded to the Q¹ group,with the H of the NH group about 2 atoms adjacent to the Q¹ group, butstill available for H-bonding. In some embodiments, P¹y is absent. Insome embodiments the P¹y group has the formula:

In some aspects, P¹s is selected such that P¹s does not provide anyoverly reactive groups. P¹s may be selected so as to provide an overalllength of the P¹ groups of between 2-15 atoms. P¹s may be selected sothat the overall length of the P¹ group is between 2 and 10 atoms. X¹groups may be selected so that the overall length of P¹ group is 4-8atoms. P¹ groups may be selected so that the overall length of the P¹group is 5 atoms. P¹ groups may be selected so that the overall lengthof P¹ group is 6 atoms. In some aspects, P¹ groups may comprise one ofthe following formulae:

where n=1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, and m is present or absent; nmay be 1, 2, 3, 4, 5, or 6; n may be 1, 2, 3, or 4; n may be 1; n may be2; n may be 3; n may be 4.

P¹p ideally is selected so as to enable a specific directional covalentlinking strategy to the linking residue of a targeting molecule(TA-linking residue), such as a peptide, protein, small molecule,nucleic acid or aptamer. For example, where the TA-linking residuecomprises a nucleophilic group, P¹p may be an electrophilic group andvice versa. For example, if the TA-linking residue side chain comprisesan amine group, such as K, H, Y, orthinine, Dap, or Dab, Xp may be COOH,or other similarly reactive electrophile. If the TA-linking residue is Dor E, P¹p may comprise a nucleophilic group, such as an amine group.Either of these strategies permits a covalent bond to be formed betweenthe P¹p group and the TA-linking residue by amide bond formationstrategies. Where the TA-linking group is an amine group, P¹p maycomprise the formula:

P¹ may be an optionally present biologically compatible polymer or blockcopolymer. P¹ may be of the structure:

wherein p is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 32, 43, 44, or 45; w, r, and s are eachindependently 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19 or 20; and Rb at each occurrence is independently hydrogen,substituted or unsubstituted C₁₋₁₀ alkyl, substituted or unsubstitutedC₃₋₇ cycloalkyl-C₁₋₆ alkyl, or substituted or unsubstituted aryl-C₁₋₆alkyl.

Where the TA-linking residue is C, homologs of C, or other thiol-groupcontaining residues, P¹p may comprise a maleimide group (or similar)permitting a thiol- maleimide addition reaction strategy to covalentlylink the P¹p group to the TA-linking residue. In some aspects, P¹p mayalso comprise a thiol group, allowing a disulphide bridge to be formedbetween the TA-linking residue and P¹p group. In some aspects, P¹p maybe be maleimide:

wherein the arrow indicates the point of attachment to the targetingmolecule and the parallel line represents to attachment to the Q¹ groupof the linker. Where the point of attachment to the targeting moleculecomprises a cysteine residue, or other thiol bearing side chain, themechanism of conjugation may be as follows:

In some aspects, the P¹p group comprises a substituted maleimide:

In some aspects, P¹ is

wherein v and w are selected such that the backbone length of X¹ is 6-12atoms;

In some aspects, the TA-linker is of the formula:

wherein n=1, or 2, or 3, or 4, 5, 6, 7, 8, 9, or 10; n may be 1, 2, 3,4, 5, or 6; n may be 1; n may be 2; n may be 3; n may be 4. M may beabsent. M may be present. In some aspects, TA-linker is of the formula:

wherein n=1, or 2, or 3, or 4, 5, 6, 7, 8, 9, or 10; n may be 1, 2, 3,4, 5, or 6; n may be 1; n may be 2; n may be 3; n may be 4. M may beabsent. M may be present.

In some aspects, the P¹ portion of CA-linkers may be used as the Y¹,X¹—Y¹, Y¹—Z and X¹—Y¹—Z, portion of linkers for a MAC of the invention.

Peptides and Proteins

Acyl lysine, orK_(ac) (also AcK) refers to: K_(SH) refers to: Aib (2-aminoisobutyricacid):

Generally, nomenclatures used in connection with, and techniques of,cell and tissue culture, molecular biology, immunology, microbiology,genetics and protein and nucleic acid chemistry and hybridizationdescribed herein are those well known and commonly used in the art. Themethods and techniques of the present invention are generally performedaccording to conventional methods well known in the art and as describedin various general and more specific references that are cited anddiscussed throughout the present specification unless otherwiseindicated. As used herein, the 20 natural, or conventional, amino acidsand their abbreviations follow IUPAC single letter and three lettercodes. “Polypeptide,” “peptide,” and “protein” are used interchangeablyto refer to a polymer of amino acid residues. As used herein, theseterms apply to amino acid polymers in which one or more amino acidresidues is an artificial chemical analog of a corresponding naturallyoccurring amino acid. These terms also apply to naturally occurringamino acid polymers. Amino acids can be in the L-form or D-form as longas the binding and other desired characteristics of the peptide aremaintained. A polypeptide may be monomeric or polymeric.

Unless indicated otherwise by a “D” prefix, e.g., D-Ala or N-Me-D-Ile,or written in lower case format, e.g., a, i, I, (D versions of Ala, Ile,Leu), the stereochemistry of the α-carbon of the amino acids andaminoacyl residues in peptides described in this specification and theappended claims is the natural or “L” configuration.

All peptide sequences are written according to the generally acceptedconvention whereby the α-N-terminal amino acid residue is on the leftand the α-C-terminal amino acid residue is on the right. As used herein,the term “N-terminus” refers to the free α-amino group of an amino acidin a peptide, and the term “C-terminus” refers to the free α-carboxylicacid terminus of an amino acid in a peptide. A peptide which isN-terminated with a group refers to a peptide bearing a group on theα-amino nitrogen of the N-terminal amino acid residue. An amino acidwhich is N-terminated with a group refers to an amino acid bearing agroup on the α-amino nitrogen.

As used herein, “halo,” “halogen” or “halide” refers to F, Cl, Br or I.

As used herein, “biological activity” refers to the in vivo activitiesof a compound, composition, or other mixture, or physiological responsesthat result upon in vivo administration of a compound, composition orother mixture. Biological activity thus encompasses therapeutic effects,diagnostic effects and pharmaceutical activity of such compounds,compositions, and mixtures.

The term “biologically compatible” as used herein means something thatis biologically inert or non reactive with intracellular and extracellular biological molecules, and non toxic.

The term “alkyl” by itself or as part of another term refers to astraight chain or branched, saturated hydrocarbon having the indicatednumber of carbon atoms (e.g. “C₁-C₈” alkyl refer to an alkyl grouphaving from 1 to 8 carbon atoms). When the number of carbon atoms is notindicated, the alkyl group has from 1 to 8 carbon atoms. Representativestraight chain C₁-C₈ alkyls include, but are not limited to, methyl,ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, n-heptyl and n-octyl; whilebranched C₁-C₈ alkyls include, but are not limited to, -isopropyl,-sec-butyl, -isobutyl, -tert-butyl, -isopentyl, and -2-methylbutyl;unsaturated C₂-C₈ alkyls include, but are not limited to, vinyl, allyl,1-butenyl, 2-butenyl, isobutylenyl, 1-pentenyl, 2-pentenyl,3-methyl-1-butenyl, 2-methyl-2-butenyl, 2,3-dimethyl-2-butenyl, 1-hexyl,2-hexyl, 3-hexyl, acetylenyl, propynyl, 1-butynyl, 2-butynyl,1-pentynyl, 2-pentynyl and 3-methyl-1-butynyl.

The phrase “substituted alkyl” refers to an alkyl group in which one ormore bonds to a carbon(s) or hydrogen(s) are replaced by a bond tonon-hydrogen and non-carbon atoms such as, but not limited to, a halogenatom in halides such as F, Cl, Br, and I; an oxygen atom in groups suchas hydroxyl groups, alkoxy groups, aryloxy groups, and ester groups; asulfur atom in groups such as thiol groups, alkyl and aryl sulfidegroups, sulfone groups, sulfonyl groups, and sulfoxide groups; anitrogen atom in groups such as amines, amides, alkylamines,dialkylamines, arylamines, alkylarylamines, diarylamines, N-oxides,imides, and enamines; a silicon atom in groups such as in trialkylsilylgroups, dialkylarylsilyl groups, alkyldiarylsilyl groups, andtriarylsilyl groups; and other heteroatoms in various other groups.Substituted alkyl groups also include groups in which one or more bondsto a carbon(s) or hydrogen(s) atom is replaced by a bond to a heteroatomsuch as oxygen in carbonyl, carboxyl, and ester groups; nitrogen ingroups such as imines, oximes, hydrazones, and nitriles. Substitutedalkyl groups include, among others, alkyl groups in which one or morebonds to a carbon or hydrogen atom is/are replaced by one or more bondsto fluorine atoms. One example of a substituted alkyl group is thetrifluoromethyl group and other alkyl groups that contain thetrifluoromethyl group. Other alkyl groups include those in which one ormore bonds to a carbon or hydrogen atom is replaced by a bond to anoxygen atom such that the substituted alkyl group contains a hydroxyl,alkoxy, aryloxy group, or heterocyclyloxy group. Still other alkylgroups include alkyl groups that have an amine, alkylamine,dialkylamine, arylamine, (alkyl)(aryl)amine, diarylamine,heterocyclylamine, (alkyl)(heterocyclyl)amine,(aryl)(heterocyclyl)amine, or diheterocyclylamine group.

The phrase “unsubstituted alkyl” refers to a divalent unsubstitutedalkyl group as defined above. Thus methylene, ethylene, and propyleneare each examples of unsubstituted alkylenes. The phrase “substitutedalkyl” refers to a divalent substituted alkyl group as defined above.Substituted or unsubstituted lower alkylene groups have from 1 to about6 carbons.

The phrase “unsubstituted cycloalkyl” refers to cyclic alkyl groups suchas cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, andcyclooctyl and such rings substituted with straight and branched chainalkyl groups as defined above. The phrase also includes polycyclic alkylgroups such as, but not limited to, adamantyl norbornyl, andbicyclo[2.2.2]octyl and the like, as well as such rings substituted withstraight and branched chain alkyl groups as defined above. Thus, thephrase would include methylcylcohexyl groups among others. The phrasedoes not include cyclic alkyl groups containing heteroatoms.Unsubstituted cycloalkyl groups may be bonded to one or more carbonatom(s), oxygen atom(s), nitrogen atom(s), and/or sulfur atom(s) in theparent compound. In some embodiments unsubstituted cycloalkyl groupshave from 3 to 20 carbon atoms. In other embodiments, such unsubstitutedalkyl groups have from 3 to 8 carbon atoms while in others, such groupshave from 3 to 7 carbon atoms.

The phrase “substituted cycloalkyl” has the same meaning with respect tounsubstituted cycloalkyl groups that substituted alkyl groups have withrespect to unsubstituted alkyl groups. Thus, the phrase includes, but isnot limited to, oxocyclohexyl, chlorocyclohexyl, hydroxycyclopentyl, andchloromethylcyclohexyl groups.

The term “aryl,” by itself or an part of another term, means asubstituted or unsubstituted monovalent carbocyclic aromatic hydrocarbonradical of 6-20 carbon atoms derived by the removal of one hydrogen atomfrom a single carbon atom of a parent aromatic ring system. Typical arylgroups include, but are not limited to, radicals derived from benzene,substituted benzene, naphthalene, anthracene, biphenyl, and the like. Asubstituted carbocyclic aromatic group (e.g., an aryl group) can besubstituted with one or more, preferably 1 to 5, of the followinggroups: C₁-C₈ alkyl, —O—(C₁-C₈ alkyl), —C(O)R′, —OC(O)R′, —C(O)OR′,—C(O)NH₂, —C(O)NHR′, —C(O)N(R′)₂, —NHC(O)R′, —S(O)₂R′, —S(O)R′, —OH,halogen, —N₃, —NH₂, —NH(R′), —N(R′)₂ and —CN; wherein each R′ isindependently selected from —H, C₁-C₈ alkyl and unsubstituted aryl. Insome embodiments, a substituted carbocyclic aromatic group can furtherinclude one or more of: —NHC(═NH)NH₂, —NHCONH₂, —S(═O)₂R′ and —SR′.“Arylene” is the corresponding divalent moiety.

The term “substituted alkyl” means an alkyl in which one or morehydrogen atoms are each independently replaced with a substituent.Typical substituents include, but are not limited to, —X, —R, —O—, —OR,—SR, —S⁻, —NR₂, —NR₃, ═NR, —CX₃, —CN, —OCN, —SCN, —N═C═O, —NCS, —NO,—NO₂, ═N₂, —N₃, —NRC(═O)R, —C(═O)NR₂, —SO₃ ⁻, —SO₃H, —S(═O)₂R,—OS(═O)₂OR, —S(═O)₂NR, —S(═O)R, —OP(═O)(OR)₂, —P(═O)(OR)₂, —PO₃ ²⁻,PO₃H₂, —AsO₂H₂, —C(═O)R, —C(═O)X, —C(═S)R, —CO₂R, —CO₂ ⁻, —C(═S)OR,—C(═O)SR, —C(═S)SR, —C(═O)NR₂, —C(═S)NR₂, or —C(═NR)NR₂, where each X isindependently a halogen: —F, —Cl, —Br, or —I; and each R isindependently —H, C₁-C₂₀ alkyl, C₁-C₂₀ heteroalkyl, C₆-C₂₀ aryl, C₃-C₈heterocyclyl, a protecting group or a prodrug moiety. Aryl, alkylene andheteroalkylene groups as described above may also be similarlysubstituted.

The term “aralkyl” by itself or part of another term, means an alkylgroup, as defined above, substituted with an aryl group, as definedabove.

The term “alkylene,” by itself of as part of another term, refers to asaturated, branched or straight chain or cyclic hydrocarbon radical ofthe stated number of carbon atoms, typically 1-18 carbon atoms, andhaving two monovalent radical centers derived by the removal of twohydrogen atoms from the same or two different carbon atoms of a parentalkane. Typical alkylene radicals include, but are not limited to:methylene (—CH₂—), 1,2-ethylene —CH₂CH₂—), 1,3-propylene (—CH₂CH₂CH₂—),1,4-butylene (—CH₂CH₂CH₂CH₂—), and the like. A “C₁-C₁₀” straight chainalkylene is a straight chain, saturated hydrocarbon group of the formula—(CH₂)₁₋₁₀—. Examples of a C₁-C₁₀ alkylene include methylene, ethylene,propylene, butylene, pentylene, hexylene, heptylene, ocytylene, nonyleneand decalene.

The term “heteroalkylene” by itself or as part of another substituentmeans a divalent group derived from heteroalkyl (as discussed above).For heteroalkylene groups, heteroatoms can also occupy either or both ofthe chain termini.

The term “C₃-C₈ heterocyclyl” by itself or as part of another term,refers to a monovalent substituted or unsubstituted aromatic ornon-aromatic monocyclic, bicyclic or tricyclic ring system having from 3to 8 carbon atoms (also referred to as ring members) and one to fourheteroatom ring members independently selected from N, O, P or S, andderived by removal of one hydrogen atom from a ring atom of a parentring system. One or more N, C or S atoms in the heterocyclyl can beoxidized. The ring that includes the heteroatom can be aromatic ornonaromatic. Unless otherwise noted, the heterocyclyl is attached to itspendant group at any heteroatom or carbon atom that results in a stablestructure. Representative examples of a C₃-C₈ heterocyclyl include, butare not limited to, tetrahyrofuranyl, oxetanyl, pyranyl, pyrrolidinyl,piperidinyl, benzofuranyl, benzothiophene, indolyl, benzopyrazolyl,pyrrolyl, thiophenyl (thiopene), furanyl, thiazolyl, imidazolyl,pyrazolyl, triazolyl, quinolinyl, pyrimidinyl, pyridinyl, pyridonyl,pyrazinyl, pyridazinyl, isothiazolyl, isoxazolyl and tetrazolyl. A C₃-C₈heterocyclyl can be substituted with up to seven groups including, butnot limited to, C₁-C₈ alkyl, C₁-C₈ heteroalkyl, —OR′, aryl, —C(O)R′,—OC(O)R′, —C(O)OR′, —C(O)NH₂, —C(O)NHR′, —C(O)N(R′)₂, —NHC(O)R′,—S(═O)₂R′, —S(O)R′, halogen, —N₃, —NH₂, —NH(R′), —N(R′)₂ and —CN;wherein each R′ is independently selected from —H, C₁-C₈ alkyl, C₁-C₈heteroalkyl and aryl. In some embodiments, a substituted heterocyclylcan also include one or more of: —NHC(═NH)NH₂, —NHCONH₂, —S(═O)₂R′ and—SR′. “Heterocyclo” is the corresponding divalent moiety.

The term “C₃-C₈ carbocyclyl” by itself or as part of another term, is a3-, 4-, 5-, 6-, 7- or 8-membered monovalent, substituted orunsubstituted, saturated or unsaturated non-aromatic monocyclic orbicyclic carbocyclic ring derived by the removal of one hydrogen atomfrom a ring atom of a parent ring system. Representative C₃-C₈carbocyclyl include, but are not limited to, cyclopropyl, cyclobutyl,cyclopentyl, cyclopentadienyl, cyclohexyl, cyclohexenyl,1,3-cyclohexadienyl, 1,4-cyclohexadienyl, cycloheptyl,1,3-cycloheptadienyl, 1,3,5-cycloheptatrienyl, cyclooctyl,cyclooctadienyl, bicyclo(111)pentane, and bicyclo(222)octane. A C₃-C₈carbocyclyl group can be unsubstituted or substituted with up to sevengroups including, but not limited to, C₁-C₈ alkyl, C₁-C₈ heteroalkyl,—OR′, aryl, —C(O)R′, —OC(O)R′, —C(O)OR, —C(O)NH₂, —C(O)NHR′,—C(O)N(R′)₂, —NHC(O)R′, —S(═O)₂R′, —S(═O)R′, —OH, -halogen, —N₃, —NH₂,—NH(R′), —N(R′)₂ and —CN; where each R′ is independently selected from—H, C₁-C₈ alkyl, C₁-C₈ heteroalkyl and aryl. “C₃-C₈ carbocyclo” is thecorresponding divalent moiety.

The term “heteroaralkyl” by itself or part of another term, means analkyl group, as defined above, substituted with an aromatic heterocyclylgroup, as defined above. Heteroaralclo is the corresponding divalentmoiety.

“About” or “approximately,” when used in connection with a measurablenumerical variable, refers to the indicated value of the variable and toall values of the variable that are within the experimental error of theindicated value (e.g., within the 95% confidence interval for the mean)or within 10 percent of the indicated value, whichever is greater.

“Connecting chain”, or “chain” as herein used refers to the sequences ofamino acids in any tertiary structural form other than a β-strand thatconnect the individual β-strands of an immunoglobulin domain. The termsencompass the structural motifs of α-helices, turns, loops, andβ-hairpins. The terms “α-helices”, “turns”, “loops”, and “β-hairpins”have the meaning commonly ascribed to them in the art so as to be ableto distinguish between the four distinct three dimensional structuralmotifs.

The term “identity,” as known in the art, refers to a relationshipbetween the sequences of two or more polypeptide molecules or two ormore nucleic acid molecules, as determined by comparing the sequences.In the art, “identity” also means the degree of sequence relatednessbetween polypeptide or nucleic acid molecule sequences, as the case maybe, as determined by the match between strings of nucleotide or aminoacid sequences. “Identity” measures the percent of identical matchesbetween two or more sequences with gap alignments addressed by aparticular mathematical model of computer programs (i.e. “algorithms”).

The term “similarity” is a related concept, but in contrast to“identity”, refers to a measure of similarity which includes bothidentical matches and conservative substitution matches. Sinceconservative substitutions apply to polypeptides and not nucleic acidmolecules, similarity only deals with polypeptide sequence comparisons.If two polypeptide sequences have, for example, 10 out of 20 identicalamino acids, and the remainder are all nonconservative substitutions,then the percent identity and similarity would both be 50%. If in thesame example, there are 5 more positions where there are conservativesubstitutions, then the percent identity remains 50%, but the percentsimilarity would be 75% (15 out of 20). Therefore, in cases where thereare conservative substitutions, the degree of similarity between twopolypeptide sequences will be higher than the percent identity betweenthose two sequences.

The term “conservative amino acid substitution” refers to a substitutionof a native amino acid residue with a normative residue such that thereis little or no effect on the polarity or charge of the amino acidresidue at that position. For example, a conservative substitutionresults from the replacement of a non-polar residue in a polypeptidewith any other non-polar residue.

Structural Alignment

Structural alignments, which are usually specific to protein andsometimes RNA sequences, use information about the secondary andtertiary structure of the protein or RNA molecule to aid in aligning thesequences. These methods are used for two or more sequences andtypically produce local alignments; however, because they depend on theavailability of structural information, they can only be used forsequences whose corresponding structures are known (usually throughX-ray crystallography or NMR spectroscopy). Because both protein and RNAstructure is more evolutionarily conserved than sequence, structuralalignments can be more reliable between sequences that are verydistantly related and that have diverged so extensively that sequencecomparison cannot reliably detect their similarity. Where there is noavailable structural data on one of the proteins, a comparison can stillbe made if structural data is available on one or preferably moreclosely related proteins, such as immunoglobulins across species, and inparticular antibody constant domains across species and subtype.

Structural alignments are used as the “gold standard” in evaluatingalignments for homology-based protein structure prediction because theyexplicitly align regions of the protein sequence that are structurallysimilar rather than relying exclusively on sequence information.

The DALI method, or distance matrix alignment, is a fragment-basedmethod for constructing structural alignments based on contactsimilarity patterns between successive hexapeptides in the querysequences. It can generate pairwise or multiple alignments and identifya query sequence's structural neighbors in the Protein Data Bank (PDB).It has been used to construct the FSSP structural alignment database(Fold classification based on Structure-Structure alignment of Proteins,or Families of Structurally Similar Proteins). A DALI webserver can beaccessed at EBI DALI and the FSSP is located at The Dali Database.

SSAP (sequential structure alignment program) is a dynamicprogramming-based method of structural alignment that uses atom-to-atomvectors in structure space as comparison points. It has been extendedsince its original description to include multiple as well as pairwisealignments, and has been used in the construction of the CATH (Class,Architecture, Topology, Homology) hierarchical database classificationof protein folds. The CATH database can be accessed at CATH ProteinStructure Classification.

The combinatorial extension method of structural alignment generates apairwise structural alignment by using local geometry to align shortfragments of the two proteins being analyzed and then assembles thesefragments into a larger alignment. Based on measures such as rigid-bodyroot mean square distance, residue distances, local secondary structure,and surrounding environmental features such as residue neighborhydrophobicity, local alignments called “aligned fragment pairs” aregenerated and used to build a similarity matrix representing allpossible structural alignments within predefined cutoff criteria. A pathfrom one protein structure state to the other is then traced through thematrix by extending the growing alignment one fragment at a time. Theoptimal such path defines the combinatorial-extension alignment. Aweb-based server implementing the method and providing a database ofpairwise alignments of structures in the Protein Data Bank is located atthe Combinatorial Extension website.

Sequence Alignment

Where structural alignment with sequences of the invention is notpossible, for example due to an absence of target sequence NMR orcrystal structure data, sequence alignment may be used. The skilledperson is familiar with sequence alignment tools (such as BLAST, CLUSTALand others known to the skilled person, such as those described herein),and is able to align sequences, particularly antibody constant domainsequences according to known structural motifs, especially due to thelarge number of exemplary structural studies already existent forimmunoglobulin domains, antibodies and antibody constant domains inparticular, across subtype and species.

Computational approaches to sequence alignment generally fall into twocategories: global alignments and local alignments. Calculating a globalalignment is a form of global optimization that “forces” the alignmentto span the entire length of all query sequences. By contrast, localalignments identify regions of similarity within long sequences that areoften widely divergent overall. Local alignments are often preferable,but can be more difficult to calculate because of the additionalchallenge of identifying the regions of similarity. A variety ofcomputational algorithms have been applied to the sequence alignmentproblem. These include slow but formally correct methods like dynamicprogramming and also efficient, heuristic algorithms or probabilisticmethods designed for large-scale database search, that do not guaranteeto find best matches.

Global alignments, which attempt to align every residue in everysequence, are most useful when the sequences in the query set aresimilar and of roughly equal size. A general global alignment techniqueis the Needleman-Wunsch algorithm, which is based on dynamicprogramming. Local alignments are more useful for dissimilar sequencesthat are suspected to contain regions of similarity or similar sequencemotifs within their larger sequence context. The Smith-Watermanalgorithm is a general local alignment method also based on dynamicprogramming.

Pairwise sequence alignment methods are used to find the best-matchingpiecewise (local) or global alignments of two query sequences. The threeprimary methods of producing pairwise alignments are dot-matrix methods,dynamic programming, and word methods; however, multiple sequencealignment techniques can also align pairs of sequences. Although eachmethod has its individual strengths and weaknesses, all three pairwisemethods have difficulty with highly repetitive sequences of lowinformation content—especially where the number of repetitions differ inthe two sequences to be aligned. One way of quantifying the utility of agiven pairwise alignment is the ‘maximum unique match’ (MUM), or thelongest subsequence that occurs in both query sequence. Longer MUMsequences typically reflect closer relatedness. Preferred methods todetermine identity and/or similarity are designed to give the largestmatch between the sequences tested. Methods to determine identity andsimilarity are codified in publicly available computer programs.Preferred computer program methods to determine identity and similaritybetween two sequences include, but are not limited to, the GCG programpackage, including GAP (Devereux et al., Nuc. Acids Res. 12: 387 (1984);Genetics Computer Group, University of Wisconsin, Madison, Wis.),BLASTP, BLASTN, and FASTA (Atschul et al., J. Mol. Biol. 215: 403-10(1990)). The BLAST X program is publicly available from the NationalCenter for Biotechnology Information (NCBI) and other sources (Altschulet al., BLAST Manual (NCB NLM NIH, Bethesda, Md.); Altschul et al.,1990, supra). The well-known Smith Waterman algorithm may also be usedto determine identity.

By way of example, using the computer algorithm GAP (Genetics ComputerGroup), two polypeptides for which the percent sequence identity is tobe determined are aligned for optimal matching of their respective aminoacids (the “matched span”, as determined by the algorithm). A gapopening penalty (which is calculated as 3× the average diagonal; the“average diagonal” is the average of the diagonal of the comparisonmatrix being used; the “diagonal” is the score or number assigned toeach perfect amino acid match by the particular comparison matrix) and agap extension penalty (which is usually 0.1× the gap opening penalty),as well as a comparison matrix such as PAM 250 or BLOSUM 62 are used inconjunction with the algorithm. Preferred parameters for polypeptidesequence comparison include the following: Algorithm: Needleman andWunsch, J. Mol. Biol. 48: 443-53 (1970). Comparison matrix: BLOSUM 62from Henikoff et al., Proc. Natl. Acad. Sci. U.S.A. 89: 10915-19 (1992).

Other exemplary algorithms, gap opening penalties, gap extensionpenalties, comparison matrices, thresholds of similarity, etc. may beused by those of skill in the art, including those set forth in theProgram Manual, WisconsinPackage, Version 9, September, 1997. Theparticular choices to be made will depend on the specific comparison tobe made, such as DNA to DNA, protein to protein, protein to DNA; andadditionally, whether the comparison is between given pairs of sequences(in which case GAP or BestFit are generally preferred) or between onesequence and a large database of sequences (in which case FASTA orBLASTA are preferred).

SEQUENCE LIST SEQ Description Sequence 1 Heavy ChainQVQLVESGGG LVKPGGSLRL SCAASGFTFS DYYMSWIRQA PGKGLEWVSY 2.12.1.fxISSSGSTRDY ADSVKGRFTI SRDNAKNSLY LQMNSLRAED TAVYYCVRDG CDRs underlinedVETTFYYYYY GMDVWGQGTT VTVSSASTKG PSVFPLAPCS RSTSESTAALGCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSNFGTQTYTCNV DHKPSNTKVD KTVERKCCVE CPPCPAPPVA GPSVFLFPPKPKDTLMISRT PEVTCVVVDV SHEDPEVQFN WYVDGVEVHN AKTKPREEQFNSTFRVVSVL TVVHQDWLNG KEYKCKVSNK GLPAPIEKTI SKTKGQPREPQVYTLPPSRE EMTKNQVSLT CLVKGFYPSD IAVEWESNGQ PENNYKTTPPMLDSDGSFFL YSKLTVDKSR WQQGNVFSCS VMHEALHNHY TQKSLSLSPGK 2 Light ChainDIQMTQSPSS LSASVGDRVT ITCRASQDIR RDLGWYQQKP GKAPKRLIYA 2.12.1.fxASRLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCLQ HNNYPRTFGQ CDRs underlinedGTKLVIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKVDNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC 3HC variable QVQLVESGGG LVKPGGSLRL SCAASGFTFS DYYMSWIRQA PGKGLEWVSY2.12.1.fx ISSSGSTRDY ADSVKGRFTI SRDNAKNSLY LQMNSLRAED TAVYYCVRDGVETTFYYYYY GMDVWGQGTT VT 4 HC constantVSSASTKG PSVFPLAPCS RSTSESTAAL GCLVKDYFPE PVTVSWNSGA 2.12.1.fxLTSGVHTFPA VLQSSGLYSL SSVVTVPSSN FGTQTYTCNV DHKPSNTKVDKTVERKCCVE CPPCPAPPVA GPSVFLFPPK PKDTLMISRT PEVTCVVVDVSHEDPEVQFN WYVDGVEVHN AKTKPREEQF NSTFRVVSVL TVVHQDWLNGKEYKCKVSNK GLPAPIEKTI SKTKGQPREP QVYTLPPSRE EMTKNQVSLTCLVKGFYPSD IAVEWESNGQ PENNYKTTPP MLDSDGSFFL YSKLTVDKSRWQQGNVFSCS VMHEALHNHY TQKSLSLSPGK 5 LC variableDIQMTQSPSS LSASVGDRVT ITCRASQDIR RDLGWYQQKP GKAPKRLIYA 2.12.1.fxASRLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCLQ HNNYPRTFGQ GTKLVIKR 6Human CLκ 1-106 TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN(Km(3) X⁴⁵ = A/X⁸³ = V SQESVTEQDS KDSTYSLSST LTLSKADYE K HKVYACEVTH QGLSSPVTKS K⁸⁰ bold & underlined FNRGEC 2.12.1.fx 7Human CLκ 1-106 TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNKm(1,2) X⁴⁵ = A/X⁸³ = L SQESVTEQDS KDSTYSLSST LTLSKADYE K HKLYACEVTH QGLSSPVTKS K⁸⁰ bold & underlined FNRGEC 8 Human CLκ 1-106TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNVLQSGN (Km(1) X⁴⁵ =V/X⁸³ = L SQESVTEQDS KDSTYSLSST LTLSKADYE K  HKLYACEVTH QGLSSPVTKSK⁸⁰ bold & underlined FNRGEC 9 hCLκ 1-106TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGN X⁸² = any AASQESVTEQDS KDSTYSLSST LTLSKADYEK HxxYACEVTH QGLSSPVTKS X⁴⁵ = V/A X⁸³ =L/V FNRGEC 10 Human CLκ 1-106TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGN X⁴⁵ = V/A X⁸³ =L/V SQESVTEQDS KDSTYSLSST LTLSKADYEK HKxYACEVTH QGLSSPVTKS FNRGEC 11Human CLκ 1-106 TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNX⁸² = any aa SQESVTEQDS KDSTYSLSST LTLSKADYEK HxVYACEVTH QGLSSPVTKSFNRGEC 12 Human CLk.K⁸⁰RTVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYER HKVYACEVTH QGLSSPVTKS FNRGEC 13Human CLk.K⁸²R TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HRVYACEVTH QGLSSPVTKS FNRGEC 14Human CLk.K⁸⁰R/K⁸²RTVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYER HRVYACEVTH QGLSSPVTKS FNRGEC 15Human CLk.D⁴³A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVANALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 16Human CLk.K⁸⁰A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEA HKVYACEVTH QGLSSPVTKS FNRGEC 17Human CLk.H⁸¹A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK AKVYACEVTH QGLSSPVTKS FNRGEC 18Human CLk.K⁸²A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HAVYACEVTH QGLSSPVTKS FNRGEC 19Human CLk.D⁴³A/H⁸¹ATVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVANALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK AKVYACEVTH QGLSSPVTKS FNRGEC 20Human CLk.K⁴¹A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW AVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 21Human CLk.V⁴²A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KADNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 22Human CLk.N⁴⁴A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDAALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 23Human CLk.L⁴⁶A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNAAQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 24Human CLk.Q⁴⁷A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALASGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 25Human CLk.S⁴⁸A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQAGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 26Human CLk.N⁵⁰A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGASQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 27ANG 2 binding xQxYQPLDEx DKTLYDQFML QQGx peptide X1 = COCH₃ X3 and x10 =K_(ac) X24 = NH₂ 28 Human CLk.L⁷³ATVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTASKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 29Human CLk.S⁷⁴A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLAKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 30Human CLk.K⁷⁵A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSAADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 31Human CLk.Y⁷⁸A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADAEK HKVYACEVTH QGLSSPVTKS FNRGEC 32Human CLk.E⁷⁹A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYAK HKVYACEVTH QGLSSPVTKS FNRGEC 33Human CLk.H⁸¹A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK AKVYACEVTH QGLSSPVTKS FNRGEC 34Human CLk.V⁸³A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKAYACEVTH QGLSSPVTKS FNRGEC 35Human CLk.Y⁸⁴A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVAACEVTH QGLSSPVTKS FNRGEC 36Human CLk.R¹⁰³A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNAGEC 37Human CLk.D⁷⁷A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAAYEK HKVYACEVTH QGLSSPVTKS FNRGEC 38Human CLk.D⁷⁷G TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAGYEK HKVYACEVTH QGLSSPVTKS FNRGEC 39Human CLk.D⁷⁷V TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAVYEK HKVYACEVTH QGLSSPVTKS FNRGEC 40Human CLk.D⁷⁷L TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKALYEK HKVYACEVTH QGLSSPVTKS FNRGEC 41Human CLk.D⁷⁷I TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAIYEK HKVYACEVTH QGLSSPVTKS FNRGEC 42Human CLk.D⁷⁷P TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAPYEK HKVYACEVTH QGLSSPVTKS FNRGEC 43Human CLk.D⁷⁷F TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAFYEK HKVYACEVTH QGLSSPVTKS FNRGEC 44Human CLk.D⁷⁷W TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAWYEK HKVYACEVTH QGLSSPVTKS FNRGEC 45Human CLk.D⁷⁷Y TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAYYEK HKVYACEVTH QGLSSPVTKS FNRGEC 46Human CLk.D⁷⁷H TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAHYEK HKVYACEVTH QGLSSPVTKS FNRGEC 47Human CLk.D⁷⁷M TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAMYEK HKVYACEVTH QGLSSPVTKS FNRGEC 48Human CLk.D⁷⁷C TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKACYEK HKVYACEVTH QGLSSPVTKS FNRGEC 49Human CLk.D⁷⁷S TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKASYEK HKVYACEVTH QGLSSPVTKS FNRGEC 50Human CLk.D⁷⁷T TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKATYEK HKVYACEVTH QGLSSPVTKS FNRGEC 51Human CLk.D⁷⁷Q TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAQYEK HKVYACEVTH QGLSSPVTKS FNRGEC 52Human CLk.D⁷⁷N TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKANYEK HKVYACEVTH QGLSSPVTKS FNRGEC 53Human CLk.D⁷⁷E TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAEYEK HKVYACEVTH QGLSSPVTKS FNRGEC 54Human CLk.D⁷⁷R TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKARYEK HKVYACEVTH QGLSSPVTKS FNRGEC 55Human CLk.D⁷⁷K TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKAKYEK HKVYACEVTH QGLSSPVTKS FNRGEC 56Human CLk.D⁴³A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVANALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 57Human CLλ GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVKAGVETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTEC 58 mCLκADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPRDINVKW KIDGSERQNGVLNSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC 59hAbλTest LC LightGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVET chain constantTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS region (lambda) 60hAbλTest-λκ RTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 61 hAbλTest-λκJKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNEYPREAKVQWKVIDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG EC 62hAbλTest S⁸¹H/H⁸²SGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKHSRSYSCQVTHEGSTVEKTVAPTECS 63 2.12.1.fx Fab HCQVQLVESGGG LVKPGGSLRL SCAASGFTFS DYYMSWIRQA PGKGLEWVSYISSSGSTRDY ADSVKGRFTI SRDNAKNSLY LQMNSLRAED TAVYYCVRDGVETTFYYYYY GMDVWGQGTT VTVSSASTKG PSVFPLAPCS RSTSESTAALGCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSNFGTQTYTCNV DHKPSNTKVD KTVERKCCVE 64 h38C2-IgG1 LCELQMTQSPSS LSASVGDRVT ITCRSSQSLL HTYGSPYLNW YLQKPGQSPK LLIYKVSNRF  SGVPSRFSGS GSGTDFTLTI SSLQPEDFAV YFCSQGTHLPYTFGGGTKVE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAKVQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACEVTHQGLSSPV TKSFNRGEC 65 h38C2-IgG1 HCEVQLVESGGG LVQPGGSLRL SCAASGFTFS NYWMSWVRQS PEKGLEWVSEIRLRSDNYAT HYAESVKGRF TISRDNSKNT LYLQMNSLRA EDTGIYYCKTYFYSFSYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDYFPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYICNVNHKPSNT KVDKRVEPKS CDKTHTCPPC PAPELLGGPS VFLFPPKPKDTLMISRTPEV TCVVVDVSHE DPEVKFNWYV DGVEVHNAKT KPREEQYNSTYRVVSVLTVL HQDWLNGKEY KCKVSNKALP APIEKTISKA KGQPREPQVYTLPPSREEMT KNQVSLTCLV KGFYPSDIAV EWESNGQPEN NYKTTPPVLDSDGSFFLYSK LTVDKSRWQQ GNVFSCSVMH EALHNHYTQK SLSLSPGK 66 h38C2-IgG2 HCEVQLVESGGG LVQPGGSLRL SCAASGFTFS NYWMSWVRQS PEKGLEWVSEIRLRSDNYAT HYAESVKGRF TISRDNSKNT LYLQMNSLRA EDTGIYYCKTYFYSFSYWGQ GTLVTVSSAS TKGPSVFPLA PCSRSTSEST AALGCLVKDYFPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSNFGTQTYTCNVDHKPSNT KVDKTVERKC CVECPPCPAP PVAGPSVFLF PPKPKDTLMISRTPEVTCVV VDVSHEDPEV QFNWYVDGVE VHNAKTKPRE EQFNSTFRVVSVLTVVHQDW LNGKEYKCKV SNKGLPSSIE KTISKTKGQP REPQVYTLPPSREEMTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT TPPMLDSDGSFFLYSKLTVD KSRWQQGNVF SCSVMHEALH NHYTQKSLSL SPGK 67 VL h38C2ELQMTQSPSS LSASVGDRVT ITCRSSQSLL HTYGSPYLNW YLQKPGQSPKLLIYKVSNRF SGVPSRFSGS GSGTDFTLTI SSLQPEDFAV YFCSQGTHLP YTFGGGTKVE IKR 68VH h38C2 EVQLVESGGG LVQPGGSLRL SCAASGFTFS NYWMSWVRQS PEKGLEWVSEIRLRSDNYAT HYAESVKGRF TISRDNSKNT LYLQMNSLRA EDTGIYYCKTYFYSFSYWGQ GTLVTVSS 69 VL m38C2DVVMTQTPLS LPVRLGDQAS ISCRSSQSLL HTYGSPYLNW YLQKPGQSPKLLIYKVSNRF SGVPDRFSGS GSGTDFTLRI SRVEAEDLGV YFCSQGTHLP YTFGGGTKLE IK 70VH m38C2 EVKLVESGGG LVQPGGTMKL SCEISGLTFR NYWMSWVRQS PEKGLEWVAEIRLRSDNYAT HYAESVKGKF TISRDDSKSR LYLQMNSLRT EDTGIYYCKYYFYSFSYWGQ GTLVTVSA 71 Trastuzumab HCEVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVARIYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWGGDGFYAMDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVKDYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQTYICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG PSVFLFPPKPKDTLMISRTP EVTCVVVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYNSTYRVVSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQVYTLPPSREE MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPVLDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK 72 Trastuzumab VHEVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVARIYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWGGDGFYAMDYW GQGTLVTVSS 73 Trastuzumab CHASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGVHTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEPKSCDKTHTCP PCPAPELLGG PSVFLFPPKP KDTLMISRTP EVTCVVVDVSHEDPEVKFNW YVDGVEVHNA KTKPREEQYN STYRVVSVLT VLHQDWLNGKEYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSREE MTKNQVSLTCLVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRWQQGNVFSCSV MHEALHNHYT QKSLSLSPGK 74 Trastuzumab LCDIQMTQSPSS LSASVGDRVT ITCRASQDVN TAVAWYQQKP GKAPKLLIYSASFLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQQ HYTTPPTFGQGTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKVDNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC75 Trastuzumab VL DIQMTQSPSS LSASVGDRVT ITCRASQDVN TAVAWYQQKP GKAPKLLIYSASFLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQQ HYTTPPTFGQ GTKVEIKR 76Trastuzumab CL TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 77Trastuzumab D77A CLTVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKA A YEK HKVYACEVTH QGLSSPVTKS FNRGEC 78Trastuzumab D77x CLTVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGN X45 = V/A; X77 =A, G, SQESVTEQDS KDSTYSLSST LTLSKA x YEK HKVYACEVTH QGLSSPVTKSI, V, L, R, S, T, Q, FNRGEC P, N, M, H, W; X83 = V/L 79 (Gly₄ Ser)₃GGGGSGGGG SGGGGS 80 Test peptide-1 GRGDSPK 81 Test peptide-2DVPKSDQFVG LM 82 Cleavage example SKADYEK HKVYACEVTH QGLSSPVTKS 83Trypsin cleavage ADYEK HK product 1 84 Trypsin cleavageHKVYACEVTH QGLSSPVTK product 2 85 2.12.1.fx.LC.FORCAA CAA GAT CTG CCA CCA TGG ACA TGA GGG T 86 2.12.1.fx.LC.REVCAA CAG CTA GCC TAA CAC TCT CCC CTG TTG A 87 L181A.FORCAA CAG GTC TCG GCC AGC AAA GCA GAC TAC GAG AA 88 L181A.REVCAA CAG GTC TCC TGG CCG TCA GGG TGC TGC TGA G 89 TRAST.VL.FORCAA CAG GTC TCA GAT CTG CCA CCA TGG GAT GGA GC 90 TRAST.VL.REVCAA CAG GTC TCA TCC GCT TGA TTT CCA CCT TG 91 TRAST.CL.D185A.FORCAA CAG GTC TCA CGG ACC GTG GCC GCT CC 92 TRAST.CL.D185A.REVCAA CAG CTA GCC TAT CAG CAC TCG CCC CG 93 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKADxSPxx X6 = N/A; X8 =S/T; xGVETTxPSK QSNNxYAASS YLSLTPEQWx SHxSYSCxVT HEGSTVEKTV x23 =K/S/R/Q/E; APxECS x37 = A/V; X39 = T/K; X46 = S/G; x49 = V/A/I; x50 =K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x80 = K/Q; x83 = K/R; x88 =Q/L; x103 = A/T 94 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKADxSPxx S81KxGVETTxPSK QSNNxYAASS YLSLTPEQWx KHxSYSCxVT HEGSTVEKTV X6 = N/A; X8 =S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; X46 = S/G; x49 =V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x80 = K/Q; x83 =K/R; x88 = Q/L; x103 = A/T 95 CLλ consensus;GQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKADxSPxx K80X/S81KxGVETTxPSK QSNNxYAASS YLSLTPEQWx KHxSYSCxVT HEGSTVEKTV X6 = N/A; X8 =S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; X46 = S/G; x49 =V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x80 = G,A, I, L, V, S, T, M, N, Q, F, Y, W, D, or E x83 = K/R; x88 = Q/L; x103 =A/T 96 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKADxSPxx E77x/ S81ΔxGVETTxPSK QSNNxYAASS YLSLTPxQWK -HxSYSCxVT HEGSTVEKTV X6 = N/A; X8 =S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; X46 = S/G; x49 =V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x⁷⁷ =R/L/S/G/Q/P/N/V/I/T/ M; x83 = K/R; x88 = Q/L; x103 = A/T 97 CLλconsensus; GQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKADxSPxxE⁷⁷x/K⁸⁰X/S⁸¹K xGVETTxPSK QSNNxYAASS YLSLTPxQWx KHxSYSCxVT HEGSTVEKTVX6 = N/A; X8 = S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; X46 =S/G; x49 = V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x77 =R, L, S, G, Q, P, N, V, I, T, and M x80 = G, A, I, L, V,S, T, M, N, Q, F, Y, W, D, or E x83 = K/R; x88 = Q/L; x103 = A/T 98 X¹ =any aa; X² = A, xxxxKH G, I, V, L, R, S, T, Q, P, N, M, H, W; X³ =any aa; X4 = any aa. 99 X¹ = any aa; X² = A, xxxxKH G, I, L, R, S, T, P,N, M; X³ = any aa; X⁴ = any aa. 100 X¹ = any aa; X² = A, xxxxKHG, I, L, S, T, P, M; X³ = any aa; X⁴ = any aa. 101 X³ = A, G, I, V, L,KAxYEKH R, S, T, Q, P, N, M, H, W. 102 X³ = A, G, I, L, R, KAxYEKHS, T, P, N, M. 103 X³ = A, G, I, L, S, KAxYEKH T, P, M. 104 hCLκ1-106 X⁴⁵ = V/A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGNx⁷⁷ = A, G, I, V, L,SQESVTEQDS KDSTYSLSST LTLSKAxYEK HxxYACEVTH QGLSSPVTKSR, S, T, Q, P, N, M, FNRGEC H, W; X⁸² = any AA; X⁸³ = L/V 105 hCLκ1-106 X⁴⁵ = V/A TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGNx⁷⁷ = A, G, I, L, R,SQESVTEQDS KDSTYSLSST LTLSKAxYEK HxxYACEVTH QGLSSPVTKSS, T, P, N, M; X⁸² = FNRGEC any AA X⁸³ = L/V 106 hCLκ 1-106 X⁴⁵ = V/ATVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGN x⁷⁷ =A, G, I, L, S, SQESVTEQDS KDSTYSLSST LTLSKAxYEK HxxYACEVTH QGLSSPVTKST, P, M; X⁸² = any AA FNRGEC X⁸³ = L/V 107 Human CLk.D⁴³ETVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVENALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 108Human CLk.D⁴³N TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVNNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 109Human CLk.D⁴³L TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVLNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC 110Human CLk.H⁸¹N TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK NKVYACEVTH QGLSSPVTKS FNRGEC 111Human CLk.H⁸¹Q TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK QKVYACEVTH QGLSSPVTKS FNRGEC 112Human CLk.H⁸¹Y TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK YKVYACEVTH QGLSSPVTKS FNRGEC 113Human CLk.H⁸¹W TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK WKVYACEVTH QGLSSPVTKS FNRGEC 114Human CLk.H⁸¹F TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKADYEK FKVYACEVTH QGLSSPVTKS FNRGEC 115 X¹ =any aa; X² = any xxxxxKH aa; X³ = A, G, I, V, L, R, S, T, Q, P, N,M, H, W; X⁴ = any aa; X⁵ = any aa. 116 X¹ = any aa; X² = any xxxxxKHaa; X³ = A, G, I, L, R, S, T, P, N, M; X⁴ = any aa; X⁵ = any aa. 117X¹ = any aa; X² = any xxxxxKH aa; X³ = A, G, I, L, S, T, P, M; X⁴ = anyaa; X⁵ = any aa. 118 X¹ = any aa; X² = any xxxxxKH aa; X³ = A, G, I, V,L, R, S, T, Q, P, N, M, H, W; X⁴ = any aromatic amino acid; X⁵ = any aa.119 hCLκ 1-106 x43 = D, E,TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGN N, Q; X⁴⁵ =V/A; x76 = SQESVTEQDS KDSTYSLSST LTLSKxxxxK HxxYACEVTH QGLSSPVTKSany aa; x77 = A, G, FNRGEC I, V, L, R, S, T, Q, P, N, M, H, W; x78 =any aa; x79 = any aa; X⁸² = any AA; X⁸³ = L/V 120 hCLκ 1-106 x43 = D, E,TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGN N, Q; X⁴⁵ =V/A; x76 = SQESVTEQDS KDSTYSLSST LTLSKxxxxK HxxYACEVTH QGLSSPVTKSany aa; x⁷⁷ = A, G, FNRGEC I, V, L, R, S, T, Q, P, N, M, H, W; x78 =any aromatic aa; x79 = any aa; X⁸² = any AA; X⁸³ = L/V 121 hCLκ1-106 x43 = D, E, TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGNN, Q; X⁴⁵ = V/A; x76 =SQESVTEQDS KDSTYSLSST LTLSKxxxxK HxxYACEVTH QGLSSPVTKS any aa; x⁷⁷ =A, G, FNRGEC I, L, S, T, P, M; x78 = any aa; x79 = any aa; X⁸² = any AA;X⁸³ = L/V 122 hCLκ 1-106 x43 = D, E,TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNxLQSGN N, Q; X⁴⁵ =V/A; x76 = SQESVTEQDS KDSTYSLSST LTLSKxxxxK HxxYACEVTH QGLSSPVTKSany aa; x⁷⁷ = A, G, FNRGEC I, L, S, T, P, M; x78 = any aromaticaa; x79 = any aa; X⁸² = any AA; X⁸³ = L/V 123 X¹ = any aa; X² = A,xxxxKH G, I, V, L, R, S, T, Q, P, N, M; X³ = any aa; X⁴ = any aa. 124X¹ = any aa; X² = A, xxxxKH G, I, V, L, R, S, T, P, M; X³ = any aa; X⁴ =any aa. 125 X¹ = any aa; X² = A, xxxxKH G, I, V, L, S, T, M; X³ =any aa; X⁴ = any aa. 126 X¹ = any aa; X² = A, xxxxKHG, I, L, S, T, M; X³ = any aa; X⁴ = any aa. 127 kappa light chainTVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV A NALQSGN D⁴³A/D⁷⁷ASQESVTEQDS KDSTYSLSST LTLSKA A YEK HKVYACEVTH QGLSSPVTKS FNRGEC 128Human CLk D77A/H81ATVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGNSQESVTEQDS KDSTYSLSST LTLSKA A YEK  A KVYACEVTH QGLSSPVTKS FNRGEC 129Human CLk TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KV A NALQSGND43A/D77A/H81A SQESVTEQDS KDSTYSLSST LTLSKA A YEK  AKVYACEVTH QGLSSPVTKS FNRGEC 130 Rabbit CLκRDPVAPTVLI FPPAADQVAT GTVTIVCVAN KYFPDVTVTW EV D GTTQTTGIENSKTPQNS ADCTYNLSST LTLTSTQYN S   H KEYTCKVTQ GTTSVVQSFN RGDC 131Rabbit Constant GQPKAPSVFP LAPCCGDTPS STVTLGCLVK GYLPEPVTVT WNSGTLTNGVHeavy Chain RTFPSVRQSS GLYSLSSVVS VTSSSQPVTC NVAHPATNTK VDKTVAPSTC rCHSKPTCPPPEL LGGPSVFIFP PKPKDTLMIS RTPEVTCVVV DVSQDDPEVQFTWYINNEQV RTARPPLREQ QFNSTIRVVS TLPIAHQDWL RGKEFKCKVHNKALPAPIEK TISKARGQPL EPKVYTMGPP REELSSRSVS LTCMINGFYPSDISVEWEKN GKAEDNYKTT PAVLDSDGSY FLYSKLSVPT SEWQRGDVFTCSVMHEALHN HYTQKSISRS PGK 132 Trastuzumab -rabbitDIQMTQSPSS LSASVGDRVT ITCRASQDVN TAVAWYQQKP GKAPKLLIYS k1 chimera (variable ASFLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQQ HYTTPPTFGQ domain )GTKVEIK RDP VAPTVLIFPP AADQVATGTV TIVCVANKYF PDVTVTWEVD rTrast-LCGTTQTTGIEN SKTPQNSADC TYNLSSTLTL TSTQYNSHKE YTCKVTQGTT SVVQSFNRGD C 133Trastuzumab rabbitEVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVAR IgG chimeraIYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWG ( variable domain) GDGFYAMDYW GQGTLVTVSS  GQPKAPSVFP LAPCCGDTPS STVTLGCLVK rTrast-HCGYLPEPVTVT WNSGTLTNGV RTFPSVRQSS GLYSLSSVVS VTSSSQPVTCNVAHPATNTK VDKTVAPSTC SKPTCPPPEL LGGPSVFIFP PKPKDTLMISRTPEVTCVVV DVSQDDPEVQ FTWYINNEQV RTARPPLREQ QFNSTIRVVSTLPIAHQDWL RGKEFKCKVH NKALPAPIEK TISKARGQPL EPKVYTMGPPREELSSRSVS LTCMINGFYP SDISVEWEKN GKAEDNYKTT PAVLDSDGSYFLYSKLSVPT SEWQRGDVFT CSVMHEALHN HYTQKSISRS PGK 134 Rabbit CLκ-S80KRDPVAPTVLI FPPAADQVAT GTVTIVCVAN KYFPDVTVTW EV D GTTQTTGIENSKTPQNS ADCTYNLSST LTLTSTQYN K   H KEYTCKVTQ GTTSVVQSFN RGDC 135Trastuzumab -rabbitDIQMTQSPSS LSASVGDRVT ITCRASQDVN TAVAWYQQKP GKAPKLLIYS k1 chimeraASFLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQQ HYTTPPTFGQ S188K( variableGTKVEIK RDP VAPTVLIFPP AADQVATGTV TIVCVANKYF PDVTVTWEVD domain )GTTQTTGIEN SKTPQNSADC TYNLSSTLTL TSTQYN K HKE YTCKVTQGTTrTrastLC-[rCLk-S80K] SVVQSFNRGD C 136 hIL22 LCQAVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYGVHWYQQ LPGTAPKLLIYGDSNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYYC QSYDNSLSGYVFGGGTQLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVTVAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQVTHEGSTVEKT VAPTECS 137 hIL22 HCQVQLVQSGAE VKKPGASVKV SCKASGYTFT NYYMHWVRQA PGQGLEWVGWINPYTGSAFY AQKFRGRVTM TRDTSISTAY MELSRLRSDD TAVYYCAREPEKFDSDDSDV WGRGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLVKDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQTYICNVNHKP SNTKVDKKVE PKSCDKTHTC PPCPAPELLG GPSVFLFPPKPKDTLMISRT PEVTCVVVDV SHEDPEVKFN WYVDGVEVHN AKTKPREEQYNSTYRVVSVL TVLHQDWLNG KEYKCKVSNK ALPAPIEKTI SKAKGQPREPQVYTLPPSRE EMTKNQVSLT CLVKGFYPSD IAVEWESNGQ PENNYKTTPPVLDSDGSFFL YSKLTVDKSR WQQGNVFSCS VMHEALHNHY TQKSLSLSPG K 138 hIL22 VLQAVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYGVHWYQQ LPGTAPKLLIYGDSNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYYC QSYDNSLSGY VFGGGTQLTV L 139hIL22 lambda GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVKconstant AGVETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS140 hIL22-[CLλ-S⁸¹K] GQPKA APSVTLFPPS SEELQANKAT LVCLISDFYP GAVTVAWKADSSPVKAGVET TTPSKQSNNK YAASSYLSLT PEQWK K HRSY SCQVTHEGST VEKTVAPTEC S141 hIL22- GQPKA APSVTLFPPS SEELQANKAT LVCLISDFYP GAVTVAWKAD[CLλ-Q⁷⁸A /S⁸¹K] SSPVKAGVET TTPSKQSNNK YAASSYLSLT PE A WK KHRSY SCQVTHEGST VEKTVAPTEC S 142 hIL22-[CLλ-A⁴⁴V/S⁸¹K]GQPKA APSVTLFPPS SEELQANKAT LVCLISDFYP GAVTVAWK V DSSPVKAGVET TTPSKQSNNK YAASSYLSLT PEQWK K HRSY SCQVTHEGST VEKTVAPTEC S143 hIL22- GQPKA APSVTLFPPS SEELQANKAT LVCLISDFYP GAVTVAWK V D[CLλ-A⁴⁴V/Q⁷⁸A/S⁸¹K] SSPVKAGVET TTPSKQSNNK YAASSYLSLT PE A WK KHRSY SCQVTHEGST VEKTVAPTEC S 144 hIL22-GQPKA APSVTLFPPS SEELQANKAT LVCLISDFYP GAVTVAWKAD [CLλ-λ⁷⁶⁻⁸⁴/145]SSPVKAGVET TTPSKQSNNK YAASSYLSLT  KAAYEKHKV Y SCQVTHEGST VEKTVAPTEC S145 CLκ 9-aa loop KAAYEKHKV 146 Trastuzumab LC K188ADIQMTQSPSS LSASVGDRVT ITCRASQDVN TAVAWYQQKP GKAPKLLIYS (variable domain)ASFLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQQ HYTTPPTFGQGTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKVDNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYE A HK VYACEVTHQG LSSPVTKSFN RGEC147 hIGg1-CH1 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGVHTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKV 148 hIGg1-CH1-m1ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGVHTFPAVLQSS GLYSLSSVVT VPSSSEKHKV YICNVNHKPS NTKVDKKV 149hIGg1-CH1-m1-D44 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNS DGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSS EKHK V YICNVNHKP SNTKVDKKV 150hIGg1-CH1-m2 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGVHTFPAVLQSS GLYSLSSVVT VPSSS YEKHK V YICNVNHKP SNTKVDKKV 151hIGg1-CH1-m2-D44 ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNS DGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSS YEKH KV YICNVNHK PSNTKVDKKV 152hIGg1-CH1 Δ fragment LGTQT 153 M1 insert fragment EKHKV 154M2 insert fragment YEKHKV 155 hIGg1-CH2APELLGGPSV FLFPPKPKDT LMISRTPEVT CVVVDVSHED PEVKFNWYVDGVEVHNAKTK PREEQYNSTY RVVSVLTVLH QDWLNGKEYK CKVSNKALPA PIEKTISKAK 156hIGg1-CH2m APELLGGPSV FLFPPKPKDT LMISRTPEVT CVVVDVSHED PEVKFNWYVDGVEVHNAKTK PREEQYNSTY RVVSVLTVLH QDWL KH KEYK CKVSNKALPA PIEKTISKAK 157hIGg1-H3 GQPREPQVYT LPPSREEMTK NQVSLTCLVK GFYPSDIAVE WESNGQPENNYKTTPPVLDS DGSFFLYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPGK 158hIGg1-CH3m GQPREPQVYT LPPSREEMTK NQVSLTCLVK GFYPSDIAVE WESNGQPENNYKTTPPVLDS DGSFFLYSKL TVDKSRWQ KH  NVFSCSVMHE ALHNHYTQKS LSLSPGK 159Trastuzumab CH1-m2EVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVARIYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWGGDGFYAMDYW GQGTLVTVSS  ASTKGPSVFP LAPSSKSTSG GTAALGCLVKDYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSS YEKHK VYICNVNHKP SNTKVDKKVE PKSCDKTHTC PPCPAPELLG GPSVFLFPPKPKDTLMISRT PEVTCVVVDV SHEDPEVKFN WYVDGVEVHN AKTKPREEQYNSTYRVVSVL TVLHQDWLNG KEYKCKVSNK ALPAPIEKTI SKAKGQPREPQVYTLPPSRE EMTKNQVSLT CLVKGFYPSD IAVEWESNGQ PENNYKTTPPVLDSDGSFFL YSKLTVDKSR WQQGNVFSCS VMHEALHNHY TQKSLSLSPG K 160Trastuzumab CH1-m1-EVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVAR D44IYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWGGDGFYAMDYW GQGTLVTVSS  ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNS DGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSS EKHK VYICNVNHKP SNTKVDKKVE PKSCDKTHTC PPCPAPELLG GPSVFLFPPKPKDTLMISRT PEVTCVVVDV SHEDPEVKFN WYVDGVEVHN AKTKPREEQYNSTYRVVSVL TVLHQDWLNG KEYKCKVSNK ALPAPIEKTI SKAKGQPREPQVYTLPPSRE EMTKNQVSLT CLVKGFYPSD IAVEWESNGQ PENNYKTTPPVLDSDGSFFL YSKLTVDKSR WQQGNVFSCS VMHEALHNHY TQKSLSLSPG K 161Trastuzumab CH1-m2-EVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVAR D44IYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWGGDGFYAMDYW GQGTLVTVSS  ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNS DGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSS YEKH KVYICNVNHK PSNTKVDKKV EPKSCDKTHT CPPCPAPELL GGPSVFLFPPKPKDTLMISR TPEVTCVVVD VSHEDPEVKF NWYVDGVEVH NAKTKPREEQYNSTYRVVSV LTVLHQDWLN GKEYKCKVSN KALPAPIEKT ISKAKGQPREPQVYTLPPSR EEMTKNQVSL TCLVKGFYPS DIAVEWESNG QPENNYKTTPPVLDSDGSFF LYSKLTVDKS RWQQGNVFSC SVMHEALHNH YTQKSLSLSP GK 162Trastuzumab CH2m EVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVARIYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWGGDGFYAMDYW GQGTLVTVSS  ASTKGPSVFP LAPSSKSTSG GTAALGCLVKDYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQTYICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG PSVFLFPPKPKDTLMISRTP EVTCVVVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYNSTYRVVSVLT VLHQDWL KH K EYKCKVSNKA LPAPIEKTIS KAKGQPREPQVYTLPPSREE MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPVLDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK 163Trastuzumab CH3m EVQLVESGGG LVQPGGSLRL SCAASGFNIK DTYIHWVRQA PGKGLEWVARIYPTNGYTRY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCSRWGGDGFYAMDYW GQGTLVTVSS  ASTKGPSVFP LAPSSKSTSG GTAALGCLVKDYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQTYICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG PSVFLFPPKPKDTLMISRTP EVTCVVVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYNSTYRVVSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQVYTLPPSREE MTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPVLDSDGSFFLY SKLTVDKSRW Q KH NVFSCSV MHEALHNHYT QKSLSLSPGK 164Ex4 homologue x2 is HxEGTFTSDL SKQ x EEEAVR LFIEWLKNGG PSSGAPPPS AibX14 = KSH 165 hIgG1-CH1-ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WKVDNALATS T78K/Q79K/CD loopGVHTFPAVLQ SSGLYSLSSV VTVPSSSEKH KVYICNVNHK PSNTKVDKKV swap 166hIgG1-CH1-CD insert KVDNALA 167 hIGg1-CH2m-APELLGGPSV FLFPPKPKDT LMISRTPEVT CVVVDVSHED PEVKFNWYVD D82A/N85K/G86HGVEVHNAKTK PREEQYNSTY RVVSVLTVLH Q A WL KH KEYK CKVSNKALPA PIEKTISKAK168 hIGg1-CH3m-CD1/EF GQPREPQVYT LPPSREEMTK NQVSLTCLVK GFYPSDIAVE WE VDGQPENN YKTTPPVLDS DGSFFLYSKL TVDKS A WQKH NVFSCSVMHE ALHNHYTQKS LSLSPGK169 hIGg1-CH3m-CD2/EF GQPREPQVYT LPPSREEMTK NQVSLTCLVK GFYPSDIAVE WE LEGQPENN YKTTPPVLDS DGSFFLYSKL TVDKS A WQ KH  NVFSCSVMHE ALHNHYTQKSLSLSPGK 170 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 not cys K, R, H, D, E, G, P. X² = A, G, I, V, L,R, S, T, Q, P, N, M, H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E, G, P; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E, G, P; 171 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 not Cys, Pro K, R, H, D, E, G. X² = A, G, I, V, L,R, S, T, Q, P, N, M, H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E, G; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E, G; 172 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 no Cis, Pro, Gly K, R, H, D, E. X² = A, G, I, V, L,R, S, T, Q, P, N, M, H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E;173 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is not A or V X² = A, G, I, V, L, R, S, T, Q, P, N, M,H, W. X³ = L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 174 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is not A or V, S or T X² = A, G, I, V, L,R, S, T, Q, P, N, M, H, W. X³ = L, I, F, W, Y, M, N, Q, K, R, H, D, E;X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 175 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is not A, V, S or T, M, K, R, H X² = A, G, I, V, L,R, S, T, Q, P, N, M, H, W. X³ = L, I, F, W, Y, N, Q, D, E; X⁴ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 176 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is not C, G, P, A, V, S or T, M, K, R, H, N, Q, D,X² = A, G, I, V, L, or E; R, S, T, Q, P, N, M, H, W. X³ = L, I, F, W, Y,X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 177 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is Y or W X² = A, G, I, V, L, R, S, T, Q, P, N, M,H, W. X³ = L, I, F, W, Y, X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; 178 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 not C, P, G K, R, H, D, E. X4 is not F, Y, W X² =A, G, I, V, L, R, S, T, Q, P, N, M, H, W. X³ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, S,T, M, N, Q, K, R, H, D, E; 179 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X4 is not F, W, Y, H X² = A, G, I, V, L, R, S, T, Q, P, N, M, H, W. X³ =A, V, L, I, S, T, M, N, Q, K, R, D, E; X⁴ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; 180 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X3 is not A or V X² = A, G, I, V, L, X4 is not F, Y, WR, S, T, Q, P, N, M, H, W. X³ = L, I, F, W, Y, S, T, M, N, Q, K, R,H, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, H, D, E; 181 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is not A or V, S or T X² = A, G, I, V, L,X4 is not F, Y, W R, S, T, Q, P, N, M, H, W. X³ = L, I, F, W, Y,M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, H, D, E;182 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is not A, V, S or T, M, K, R, H X² = A, G, I, V, L,X4 is not F, Y, W, or H R, S, T, Q, P, N, M, H, W. X³ = L, I, F, W, Y,N, Q, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, D, E; 183 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is not C, G, P, A, V, S or T, M, K, R, H, N, Q, D,X² = A, G, I, V, L, or E; R, S, T, Q, P, N, M, X4 is not F, Y, W, or HH, W. X³ = L, I, F, W, Y, X⁴ = A, V, L, I, S, T, M, N, Q, K, R, D, E;184 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X3 is Y or W X² = A, G, I, V, L,X4 is E, K, D, R, N, or Q. R, S, T, Q, P, N, M, H, W. X³ =L, I, F, W, Y, X⁴ = N, Q, K, R, D, E; 185 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X4 is E, K, D, R, N, or Q. X² = A, G, I, V, L, R, S, T, Q, P, N, M,H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ =N, Q, K, R, D, E; 186 X¹ = A, V, L, I, S, xxxxKH T, M, N, Q, K, R, H,X1 X3 X4 not C, P, G D, E. X1 is not aromatic X² = A, G, I, V, L,R, S, T, Q, P, N, M, H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E;187 X¹ = A, V, L, I, S, xxxxKH T, M, N, Q, R, H, D, X1 X3 X4 not C, P, GE. X1 is not aromatic or K X² = A, G, I, V, L, R, S, T, Q, P, N, M,H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 188 X¹ =A, V, L, I, S, xxxxKH T, M, N. X1 X3 X4 no c, p, g X² = A, G, I, V, L,X1 is not aromatic or K, or charged R, S, T, Q, P, N, M, H, W. X³ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; 189 X¹ = A, V, L, I, M. xxxxKH X² =A, G, I, V, L, X1 X3 X4 not C, P, G R, S, T, Q, P, N, M,X1 is hydrophilic H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E;190 X¹ = A, V, L, I, S, xxxxKH T, M, N, Q, K, R, H, X1 X3 X4 not C, P, GD, E. X1 is not aromatic X² = A, G, I, V, L, X4 is not F, Y, WR, S, T, Q, P, N, M, H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, H, D, E; 191 X¹ =A, V, L, I, S, xxxxKH T, M, N, Q, K, R, H, X1 X3 X4 not C, P, G D, E.X1 is not aromatic X² = A, G, I, V, L, X4 is not F, W, Y, HR, S, T, Q, P, N, M, H, W. X³ = A, V, L, I, S, T, M, N, Q, K, R, D, E;X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 192 X¹ =A, V, L, I, S, xxxxKH T, M, N, Q, K, R, H, X1 X3 X4 not C, P, G D, E.X1 is not aromatic X² = A, G, I, V, L, X3 is not A or VR, S, T, Q, P, N, M, X4 is not F, Y, W H, W. X³ = L, I, F, W, Y,S, T, M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, H,D, E; 193 X¹ = A, V, L, I, S, xxxxKH T, M, N, Q, R, H, D,X1 X3 X4 not C, P, G E. X1 is not aromatic or K X² = A, G, I, V, L,X3 is not A or V, S or T R, S, T, Q, P, N, M, X4 is not F, Y, W H, W.X³ = L, I, F, W, Y, M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, S,T, M, N, Q, K, R, H, D, E; 194 X¹ = A, V, L, I, S, xxxxKH T, M, N, Q.X1 X3 X4 not C, P, G X² = A, G, I, V, L,X1 is not aromatic, K or charged R, S, T, Q, P, N, M,X3 is not A, V, S or T, M, K, R, H H, W. X4 is not F, Y, W, or H X³ =L, I, F, W, Y, N, Q, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, D, E;195 X¹ = A, V, L, I. xxxxKH X² = A, G, I, V, L, X1 X3 X4 not C, P, GR, S, T, Q, P, N, M, X1 is hydrophilic H, W.X3 is not C, G, P, A, V, S or T, M, K, R, H, N, Q, D, X³ =L, I, F, W, Y, or E; X⁴ = A, V, L, I, S, X4 is not F, Y, W, or HT, M, N, Q, K, R, D, E; 196 X¹ = A, V, L, I. xxxxKH X² = A, G, I, V, L,X1 X3 X4 not C, P, G R, S, T, Q, P, N, M, X1 is hydrophilic H, W.X3 is Y or W X³ = L, I, F, W, Y, X4 is E, K, D, R, N, or Q. X⁴ =N, Q, K, R, D, E; 197 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 not C, P, G K, R, H, D, E. X2 is not W X² = A, G, I, V, L,X4 is not F, Y, W R, S, T, Q, P, N, M, H. X³ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, S,T, M, N, Q, K, R, H, D, E; 198 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E. X2 is not WX² = A, G, I, V, L, X4 is not F, W, Y, H R, S, T, Q, P, N, M, H, W. X³ =A, V, L, I, S, T, M, N, Q, K, R, D, E; X⁴ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; 199 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E, G, P.X2 is not W X² = A, G, I, V, L, R, S, T, Q, P, N, M, H, W. X³ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E, G, P; X⁴ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E, G, P; 200 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E, G. X2 is not W X² = A, G, I, V, L, R, S, T, Q, P, N, M,H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E, G; X⁴ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E, G; 201 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X2 is not W X² = A, G, I, V, L, R, S, T, Q, P, N, M,H, W. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 202 X¹ =A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X2 is not W X² = A, G, I, V, L, X3 is not A or VR, S, T, Q, P, N, M, H, W. X³ = L, I, F, W, Y, S, T, M, N, Q, K, R,H, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 203X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X2 is not W, I, L, R X² = A, G, V, S, T,X3 is not A or V, S or T Q, P, N, M, H. X³ = L, I, F, W, Y,M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; 204 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 not C, P, G K, R, H, D, E. X2 is not W, I, L, R X² =A, G, V, S, T, X3 is not A, V, S or T, M, K, R, H Q, P, N, M, H. X³ =L, I, F, W, Y, N, Q, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; 205 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 not C, P, G K, R, H, D, E. X2 is A, G, P, S, T, M X² =A, G, S, T, P, X3 is not C, G, P, A, V, S or T, M, K, R, H, N, Q, D, M.or E; X³ = L, I, F, W, Y, X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; 206 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q,X1 X3 X4 not C, P, G K, R, H, D, E. X2 is A, G, P, S, T, M X² =A, G, S, T, P, X3 is Y or W M. X³ = L, I, F, W, Y, X⁴ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; 207 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X2 is A, G, P, S, T, M X² = A, G, S, T, P, X3 is not A or V M.X4 is not F, Y, W X³ = L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ =A, V, L, I, S, T, M, N, Q, K, R, H, D, E; 208 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X2 is A, G, P, S, T, M X² = A, G, S, T, P, X3 is not A or V, S or T M.X4 is not F, Y, W X³ = L, I, F, W, Y, M, N, Q, K, R, H, D, E; X⁴ =A, V, L, I, S, T, M, N, Q, K, R, H, D, E; 209 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X2 is A, G, P, S, T, M X² = A, G, S, T, P,X3 is not A, V, S or T, M, K, R, H M. X4 is not F, Y, W, or H X³ =L, I, F, W, Y, N, Q, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, D, E;210 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X2 is A, G, P, M, S, T X² = A, G, S, T, P,X3 is not C, G, P, A, V, S or T, M, K, R, H, N, Q, D, M. or E; X³ =L, I, F, W, Y, X4 is not F, Y, W, or H X⁴ = A, V, L, I, S,T, M, N, Q, K, R, D, E; 211 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X2 is A, G, P, M, S, T X² = A, G, S, T, P, X3 is Y or W M.X4 is E, K, D, R, N, or Q. X³ = L, I, F, W, Y, X⁴ = N, Q, K, R, D, E;212 X¹ = A, V, L, I, F, xxxxKH W, Y, S, T, M, N, Q, X1 X3 X4 not C, P, GK, R, H, D, E. X2 is not W or R, X² = A, G, I, V, L,X4 is E, K, D, R, N, or Q. S, T, Q, P, N, M, H. X³ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ = N, Q, K, R, D, E; 213 X¹ =A, V, L, I, S, xxxxKH T, M, N, Q, K, R, H, X1 X3 X4 not C, P, G D, E.W2 is not W or R X² = A, G, I, V, L, X1 is not aromaticS, T, Q, P, N, M, H. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E;214 X¹ = A, V, L, I, S, xxxxKH T, M, N, Q, R, H, D, X1 X3 X4 not C, P, GE. X1 is not aromatic or K X² = A, G, I, V, L, X2 is not W or RS, T, Q, P, N, M, H. X³ = A, V, L, I, F, W, Y, S, T, M, N, Q,K, R, H, D, E; X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E;215 X¹ = A, V, L, I, S, xxxxKH T, M, N. X1 X3 X4 not C, P, G X² =A, G, I, V, L, X1 is not aromatic or K, or charged S, T, Q, P, N, M, H.X2 is not W or R X³ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E;X⁴ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 216 X¹ =A, V, L, I, F, xxxxKH X² = A, G, I, V, L, X1 X3 X4 not C, P, GS, T, Q, P, N, M, H. X1 is hydrophilic X³ = A, V, L, I, F,X2 is not W or R W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, F,W, Y, S, T, M, N, Q, K, R, H, D, E; 217 X¹ = A, V, L, I, S, xxxxKHT, M, N, Q, K, R, H, X1 X3 X4 not C, P, G D, E. X1 is not aromatic X² =A, G, I, V, L, X2 is not W or R S, T, Q, P, N, M, H. X4 is not F, Y, WX³ = A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; X⁴ =A, V, L, I, S, T, M, N, Q, K, R, H, D, E; 218 X¹ = A, V, L, I, S, xxxxKHT, M, N, Q, K, R, H, X1 X3 X4 not C, P, G D, E. X1 is not aromatic X² =A, G, I, V, L, X2 is not W, or R S, T, Q, P, N, M, H.X4 is not F, W, Y, H X³ = A, V, L, I, S, T, M, N, Q, K, R, D, E; X⁴ =A, V, L, I, F, W, Y, S, T, M, N, Q, K, R, H, D, E; 219 X¹ =A, V, L, I, S, xxxxKH T, M, N, Q, K, R, H, X1 X3 X4 not C, P, G D, E.X1 is not aromatic X² = A, G, I, V, L, Is not W or RS, T, Q, P, N, M, H. X3 is not A or V X³ = L, I, F, W, Y,X4 is not F, Y, W S, T, M, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, S,T, M, N, Q, K, R, H, D, E; 220 X¹ = A, V, L, I, S, xxxxKHT, M, N, Q, R, H, D, X1 X3 X4 not C, P, G E. X1 is not aromatic or KX² = A, G, I, V, L, X2 is not W or R S, T, Q, P, N, M, H.X3 is not A or V, S or T X³ = L, I, F, W, Y, X4 is not F, Y, WM, N, Q, K, R, H, D, E; X⁴ = A, V, L, I, S, T, M, N, Q, K, R, H, D, E;221 X¹ = A, V, L, I, S, xxxxKH T, M, N, Q. X1 X3 X4 not C, P, G X² =A, G, S, T, M. X1 is not aromatic, K or charged X³ = L, I, F, W, Y,X2 is A, G, P, S, T, M N, Q, D, E; X3 is not A, V, S or T, M, K, R, HX⁴ = A, V, L, I, S, X4 is not F, Y, W, or H T, M, N, Q, K, R, D, E; 222X¹ = A, V, L, I. xxxxKH X² = A, G, S, T, M. X1 X3 X4 not C, P, G X³ =L, I, F, W, Y, X1 is hydrophilic X⁴ = A, V, L, I, S,X2 is A, G, P, S, T, M T, M, N, Q, K, R, D,X3 is not C, G, P, A, V, S or T, M, K, R, H, N, Q, D, E; or E;X4 is not F, Y, W, or H 223 X¹ = A, V, L, I. xxxxKH X² = A, G, S, T, M.X1 X3 X4 not C, P, G X³ = L, I, F, W, Y, X2 is A, G, P, S, T, M X⁴ =N, Q, K, R, D, X1 is hydrophilic E; X3 is Y or WX4 is E, K, D, R, N, or Q. 224 X¹ = A, V, L, I, F, xxxxKHW, Y, S, T, M, N, Q, X1 X3 X4 not C, P, G K, R, H, D, E.X2 is A, G, P, S, T, M X² = A, G, S, T, M.X3 is not A, V, S or T, M, K, R, H X³ = L, I, F, W, Y,X4 is not F, Y, W, or H N, Q, D, E; X⁴ = A, V, L, I, S,T, M, N, Q, K, R, D, E; 225 hCLκ 1-75 x42 = V, I,TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KxxNxLQSGN L, x43 =D, E, N, Q; SQESVTEQDS KDSTYSLSST LTLSx X⁴⁵ = V/A; x75 = any amino acid226 hCLκ 81-106 X2 = any xxYACEVTH QGLSSPVTKS FNRGEC AA; X² = L/V 227CLλ consensus GQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKADxSPxx1-76 xGVETTxPSK QSNNxYAASS YLSLTP X6 = N/A; X8 = S/T; x23 = K/S/R/Q/E;x37 = A/V; X39 = T/K; X46 = S/G; x49 = V/A/I; x50 = K/E; x51 = A/T;x57 = T/K/A; x65 = K/R/N; 228 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKxDxSPxx 1-76, x44 inc AxGVETTxPSK QSNNxYAASS YLSLTP X6 = N/A; X8 = S/T; x23 = K/S/R/Q/E; x37 =A/V; X39 = T/K; X44 is A, V, I, L X46 = S/G; x49 = V/A/I; x50 =K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; 229 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKxDxSPxx 1-76, X44 no AxGVETTxPSK QSNNxYAASS YLSLTP X6 = N/A; X8 = S/T; x23 = K/S/R/Q/E; x37 =A/V; X39 = T/K; x44 = V, I L X46 = S/G; x49 = V/A/I; x50 = K/E; x51 =A/T; x57 = T/K/A; x65 = K/R/N; 230 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKVDxSPxx 1-76, X44 = VxGVETTxPSK QSNNxYAASS YLSLTP X6 = N/A; X8 = S/T; x23 = K/S/R/Q/E; x37 =A/V; X39 = T/K; X46 = S/G; x49 = V/A/I; x50 = K/E; x51 = A/T; x57 =T/K/A; x65 = K/R/N; 231 CLλ 1-76GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKxDSSPVK X44 is A, V, I, LAGVETTTPSK QSNNKYAASS YLSLTP 232 CLλ 1-76GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKxDSSPVK X44 is V, I, LAGVETTTPSK QSNNKYAASS YLSLTP 233 CLλ 1-76GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKVDSSPVK X44 is VAGVETTTPSK QSNNKYAASS YLSLTP 234 CLλ consensus 83-103xSYSCxVTHE GSTVEKTVAP xECS x1 = K/R; x6 = Q/L; x21 = A/T 235 CLλ 83-103RSYSCQVTHE GSTVEKTVAP TECS 236 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKxDxSPxx S81K, x44 = AVIL,xGVETTxPSK QSNNxYAASS YLSLTPExWx KHxSYSCxVT HEGSTVEKTV X6 = N/A; X8 =S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; x44 A, V, I, L X46 =S/G; x49 = V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; Q78 =A/Q x80 = K/Q; x83 = K/R; x88 = Q/L; x103 = A/T 237 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKxDxSPxx S81K, X44 = VIL,xGVETTxPSK QSNNxYAASS YLSLTPExWx KHxSYSCxVT HEGSTVEKTV X6 = N/A; X8 =S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; x44 V, I, L X46 =S/G; x49 = V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; X78 =A/Q x80 = K/Q; x83 = K/R; x88 = Q/L; x103 = A/T 238 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKVDxSPxx S81K, x44 = V,xGVETTxPSK QSNNxYAASS YLSLTPExWx KHxSYSCxVT HEGSTVEKTV X6 = N/A; X8 =S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; X46 = S/G; x49 =V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x78 = A/Q x80 =K/Q; x83 = K/R; x88 = Q/L; x103 = A/T 239 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKxDxSPxx S81K, x44 =AVIL, A78 xGVETTxPSK QSNNxYAASS YLSLTPEAWx KHxSYSCxVT HEGSTVEKTV X6 =N/A; X8 = S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K;x44 A, V, I, L X46 = S/G; x49 = V/A/I; x50 = K/E; x51 = A/T; x57 =T/K/A; x65 = K/R/N; x80 = K/Q; x83 = K/R; x88 = Q/L; x103 = A/T 240 CLλconsensus GQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKxDxSPxxS81K, X44 = VIL, A78xGVETTxPSK QSNNxYAASS YLSLTPEAWx KHxSYSCxVT HEGSTVEKTV X6 = N/A; X8 =S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; x44 V, I, L X46 =S/G; x49 = V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x80 =K/Q; x83 = K/R; x88 = Q/L; x103 = A/T 241 CLλ consensusGQPKAxPxVT LFPPSSEELQ ANxATLVCLI SDFYPGxVxV AWKVDxSPxx S81K, x44 =V, A78 xGVETTxPSK QSNNxYAASS YLSLTPEAWx KHxSYSCxVT HEGSTVEKTV X6 =N/A; X8 = S/T; APxECS x23 = K/S/R/Q/E; x37 = A/V; X39 = T/K; X46 =S/G; x49 = V/A/I; x50 = K/E; x51 = A/T; x57 = T/K/A; x65 = K/R/N; x80 =K/Q; x83 = K/R; x88 = Q/L; x103 = A/T 242 CLλGQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKxDSSPVK X44 is A, V, I, LAGVETTTPSK QSNNKYAASS YLSLTPExWK  K HRSYSCQVT HEGSTVEKTV X78 is A.APTECS 243 CLλ GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKxDSSPVKX44 is V, I, L AGVETTTPSK QSNNKYAASS YLSLTPExWK  K HRSYSCQVT HEGSTVEKTVX78 is A APTECS 244 CLλGQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKVDSSPVK X44 is VAGVETTTPSK QSNNKYAASS YLSLTPExWK  K HRSYSCQVT HEGSTVEKTV X78 is A APTECS245 CD motif xxxx X1 is V, I or L X2 is D, N, Q, E X3, x4 is any AA 246CD motif xxxx X1 is V or I X2 is D, N, Q, E X3, x4 is any AA 247CD motif Vxxx X2 is D, N, Q, E X3, x4 is any AA 248 CD motif xxxxX1 is V, I or L X2 is D, or N X3, x4 is any AA 249 CD motif xxxxX1 is V, I or L X2 is Q or E X3, x4 is any AA 250 CD motif xDxxX1 is V, I or L X3, x4 is any AA 251 CD motif VDxx X3, x4 is any AA 252CD motif LExx X3, x4 is any AA 253 CD motif IExx X3, x4 is any AA 254h38C2-[LC-D185A] ELQMTQSPSS LSASVGDRVT ITCRSSQSLL HTYGSPYLNW YLQKPGQSPKLLIYKVSNRF   SGVPSRFSGS GSGTDFTLTI SSLQPEDFAV YFCSQGTHLPYTFGGGTKVE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAKVQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAA YEKHKVYACEVTHQGLSSPV TKSFNRGEC 255 CD motif xxxx X1, x2, x3, x4 = any amino acid

DETAILED DESCRIPTION OF FIGURES

FIGS. 1A, 1B, 1C, 1D: Intact molecular weight analysis of MAC by massspectrometry demonstrates that multiple peptides are attached to theanti-IGF1R antibody 2.12.1.fx. FIG. 1A: mass spectrometry data ofanti-IGF1R antibody 2.12.1.fx. FIG. 1B-1D: mass spectrometry data ofMAC-2, showing replicate experiments of 3 individual lots.

FIGS. 2A, 2B, 2C, 2D, 2E, 2F, 2G, 2H: Mass spectrometry data of2.12.1.fx (IGF1R) and 3 lots of MAC-2 (MAC) where the disulfide bondshave been reduced. FIG. 2A: Mass spectrometry data of 2.12.1.fx (IGF1R),light chain. FIG. 2B: Mass spectrometry data of 2.12.1.fx (IGF1R), heavychain. FIG. 2C: mass spectrometry data of light chain of MAC-2, lot-1.FIG. 2D: mass spectrometry data of heavy chain of MAC-2, lot-1. FIG. 2E:mass spectrometry data of light chain of MAC-2, lot-2. FIG. 2F: massspectrometry data of heavy chain of MAC-2, lot-2. FIG. 2G: massspectrometry data of light chain of MAC-2, lot-3. FIG. 2H: massspectrometry data of heavy chain of MAC-2, lot-3.

FIG. 3A: Amino acid sequence of light chain of antibody 2.12.1.fx withchymotrypsin cleavage sites noted with bullets. Chymotryptic fragmentsthat contain a Lys residue (site of potential conjugation) are labeledby number from the N-terminus. The Y15 fragment of the light chain isunderlined. FIG. 3B: Amino acid sequence of heavy chain of antibody2.12.1.fx with chymotrypsin cleavage sites noted with bullets.Chymotryptic fragments that contain a Lys residue (site of potentialconjugation) are labeled by number from the N-terminus.

FIG. 4A: Mass spectrometry data of a conjugated lysine-containingpeptide: light chain Y15, showing mass spectrometry data forunconjugated anti-IGF1R antibody 2.12.1.fx (IGF1r) and MAC-2 (MAC), aswell as a representation of the Y15 fragment. FIG. 4B: Mass spectrometrydata of un-conjugated light chain Y15 fragment, showing massspectrometry data for unconjugated anti-IGF1R antibody 2.12.1.fx (IGF1r)and MAC-2 (MAC), as well as a representation of the Y15 fragment.

FIG. 5A: The selected ion LCMS chromatogram data for the trypticfragment of 2.12.1.fx. FIG. 5B: The selected ion LCMS chromatogram datafor the tryptic fragment when LC-K¹⁸⁸ is modified with ABP of MAC-2.

FIG. 6A: The selected ion LCMS chromatogram data for the trypticfragment of 2.12.1.fx. FIG. 6B: The selected ion LCMS chromatogram datafor the tryptic peptide when LC-K¹⁹⁰ is modified with ABP of MAC-2.

FIG. 7A: Mass spectra of intact MAC-2. FIG. 7B: Mass spectra of reducedheavy chain for MAC-2. FIG. 7C: Mass spectra of reduced light chain forMAC-2.

FIG. 8A: Amino acid sequence alignment of the variable domains of m38c2,h38c2, and human germlines. Framework regions (FR) and complementaritydetermining regions (CDR) are defined according to Kabat et al.Asterisks mark differences between m38c2 and h38c2 or between h38c2 andthe human germlines.

FIG. 8B: Amino acid sequence alignment of murine constant light chainkappa region (mCLκ), human constant light chain kappa region (hCLκ), andhuman constant light chain lambda region (hCLλ). Differences betweenmCLκ and hCLκ; and between hCLκ and hCLλ; are shown as asterisks, andconserved substitutions are shown as crosses. β-strands A-G areunderlined. The turn between β-strands A and B and the α-helix betweenβ-strands E and F are each indicated in italics. Di-sulfide bond-formingcysteines between the first β-sheet (made up of β-strands ABDE; singleunderline) and the second β-sheet (made up of β-strands CGF, doubleunderline) are indicated by §. Known polymorphic loci in the humansequences are indicated in bold.

FIG. 9A: Binding ELISA data for HER2 receptor binding of trastuzumab andtrastuzumab-[CLκ-D¹⁸⁵A] conjugation products to [PEG₅-K¹¹-SEQ:27]. FIG.9B: Binding ELISA data for HER2 receptor binding of trastuzumab andtrastuzumab-[CLκ-D¹⁸⁵A] conjugation products to MMAD toxin.

FIG. 10A: representation of a constant Ig domain showing the 7 β-strandsforming the two β-sheets. FIG. 10B: close up of the α-helix betweenβ-sheets E and F.

FIG. 11. Crystal structure-based minimized ribbon representation of CLκ,showing the halo-phenyl ester reactive ‘binding site’ (small jacks)within the overall steric ‘binding pocket’ created by the 3D structure.B-strands are labeled.

FIG. 12. Crystal structure-based minimized ribbon representation of theCLκ ‘binding pocket’, showing CLκ-D⁷⁷ and CLκ-D⁴³ (as a stick model) inthe hydrogen bond with CLκ-H⁸¹ Nε or Nδ, and atomic distances in Å.

FIGS. 13A and 13B. Crystal structure-based minimized ribbonrepresentation of the CLκ and CLκ-D⁷⁷A mutant ‘binding pockets’. Thedistance between carbonyl oxygen of CLκ-D⁴³ and Nδ of CLκ-H⁸¹ differs by1 Å between the CLκ and CLκ-D⁷⁷A mutant, pointing to the predominance ofcatalytically active CLκ-H⁸¹ tautomer Nδ in the CLκ-D⁷⁷A mutant. Inaddition, the modeling identifies a clear increase in the overall sizeof the pocket in CLκ-D⁷⁷A mutant, which is represented by the figure.FIG. 13C. Crystal structure-based ribbon representation of the CLκ(grey) and CLκ-D⁷⁷A mutant (black) ‘binding pockets’ superimposed overeach other. In the CLκ-D⁷⁷A mutant, CLκ-H⁸¹ is shifted toward CLκ-D⁴³ bythe hydrogen bond interactions, as CLκ-D⁷⁷A is unable to form a hydrogenbond with Nε of CLκ-H⁸¹.

FIG. 14. Crystal structure-based minimized ribbon representation of theCLκ ‘binding pocket’. The binding site is depicted as a small jacks. Theπ electron stacking interactions with CLκ-H⁸¹ are shown, maintaining theimidazole ring at the optimum position in relation to the incominghalo-phenyl ester substrate.

FIGS. 15A and 15B. Crystal structure-based minimized ribbonrepresentation of the CLκ and CLλ ‘binding pockets. FIG. 15A shows theπ-electron interactions between CLκ-V⁴² and CLκ-H⁸¹, assisting inmaintaining the CLκ-H⁸¹ imidazole ring and the Nε electron pair at theplane needed for nucleophilic attack during catalytic reaction. Thedistance between the center of CLκ-H⁸¹ imidazole ring and each of thehydrogen atoms on the CLκ-V⁴² are 2.8 Å allowing for stronginteractions. In FIG. 15B, CLλ-A⁴⁹ is shown at a distance of 4.2 Å fromCLλ-H⁸² (identified as H81 in the figure for the purposes of clarity ofcomparison). This distance is modeled as likely too far to have asignificant influence on the position or tautomeric form of CLλ-H⁸².

FIG. 16. Sequence alignment of hCHλ1, hCHλ2, hCHλ3, hCLκ and hCLλ.β-strands of the CLκ are indicated as underlined regions. α-helices areindicated in italics.

FIG. 17. Crystal structure based alignment of sequences of hCHλ1, hCHλ2,hCHλ3, hCLκ and hCLλ according to minimized 3D homology. β-strands areindicated as boxed regions, α-helices are indicated within wavy scrolls.Key residues corresponding to CLκ-V⁴², CLκ-D⁴³, CLκ-D⁷⁷, CLκ-K⁸⁰, andCLκ-H⁸¹ are identified with rectangular dotted-line boxes extendingvertically between sequences. The crystal structure modeling of thedomains that generated this alignment suggested a short break in the Dβ-strand in the hCHλ1, hCHλ2, hCHλ3, and hCLλ domains. Other modelingand crystal structure analysis indicates that most, if not all antibodyconstant domains comprise 7 β-strands, and the D β-strand is contiguous.The two D β-strands modeled herein have accordingly been indicated as D′and D″. FIGS. 18B-31B, depicting CLλ, and CHγ domains, are orientatedsuch that the D β-strand is on the lower left of the structure pointingdownwards, and lying against the E β-strand. The D′ and D″ β-strandstogether can be seen to occupy approximately the same relative positionas the CLκ D β-strand (β-strands D and D′, D″ labelled in FIG. 18 as apoint of reference).

FIG. 18. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCLλ (B) domains.

FIG. 19. Crystal structure-based minimized ribbon representation of thehCLκ (A) and WT-hCHγ1 (B) domains.

FIG. 20. Crystal structure-based minimized ribbon representation of thehCLκ (A) and WT-hCHγ1 (B) domains, showing the sidechain location ofsignificant residues.

FIG. 21. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCHγ1-m1-D44 mutant (B) domains, showing the sidechainlocation of significant residues.

FIG. 22. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCHγ1-T78K/Q79H/CD loop swap mutant (B) domains, showingthe sidechain location of significant residues.

FIG. 23. Crystal structure-based minimized ribbon representation of thehCLκ (A) and WT-hCHγ2 (B) domains.

FIG. 24. Crystal structure-based minimized ribbon representation of thehCLκ (A) and WT-hCHγ2 (B) domains, showing the sidechain location ofsignificant residues.

FIG. 25. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCHγ2m mutant (B) domains, showing the sidechain locationof significant residues.

FIG. 26. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCHγ2m-D⁸²A mutant (B) domains, showing the sidechainlocation of significant residues.

FIG. 27. Crystal structure-based minimized ribbon representation of thehCLκ (A) and WT-hCHγ3 (B) domains.

FIG. 28. Crystal structure-based minimized ribbon representation of thehCLκ (A) and WT-hCHγ3 (B) domains, showing the sidechain location ofsignificant residues.

FIG. 29. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCHγ3m mutant (B) domains, showing the sidechain locationof significant residues.

FIG. 30. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCHγ3m CD/EF mutant (B) domains, showing the sidechainlocation of significant residues.

FIG. 31. Crystal structure-based minimized ribbon representation of thehCLκ (A) and hCHγ3m CD/EF-m2 mutant (B) domains, showing the sidechainlocation of significant residues.

FIGS. 32A and 32B. Alignment of CHγ1, CHγ2, and CHγ3 with theirrespective mutants and proposed mutant, together with CLκ and CLλ.

EXAMPLES

In order that this invention may be better understood, the followingexamples are set forth. These examples are for purposes of illustrationonly and are not to be construed as limiting the scope of the inventionin any manner.

Description of Conjugation Additions (CA), Average CA

Conjugation additions (CA) are measured on an antibody scaffold usingintact mass measurement by mass spectrometry. Upon conjugation, theoverall mass of the intact product increases by the mass and number ofadditions of the conjugated peptide, toxin, etc. If multiple additionsoccur then a distribution of conjugate forms is observed in a massspectra and the observed signal intensity of each conjugate form gives aquantitative measurement. This analysis is routinely presented in atable by listing each CA form as a percentage of all the observed CAforms. Average CA (e.g.: the overall number of CA present on a scaffold)is an additional value that describes the average conjugate load. Anexample is provided below of 2 conjugated drug products. Example 1 hasan even distribution of CA with an average CA=2.00. Example 2 has adistribution that heavily favors the presence of 2 CA with a minimalamount of other conjugation forms. The average CA is similar betweenthese examples (2.13 vs. 2.00); however, Example 1 is a moreheterogeneous product comprised of more conjugation forms, while Example2 is a more homogeneous product that contains mostly 2 CA.

TABLE 1 Average 0 CA % 1 CA % 2 CA % 3 CA % 4 CA % CA Example 1 11 22 3322 11 2.00 Example 2  2  4 77 12  5 2.13

A similar analytical treatment is also possible on these antibodyscaffolds after disulfide bonds have been reduced to generate free lightchains and heavy chains. Measurement of the intact mass of conjugatedlight/heavy chains can provide information about the location of CA onthese respective subunits.

Explanation of Directional Conjugation to CLκ-K⁸⁰

To determine site specific attachment of drug conjugates to an antibodyscaffold, a peptide map is produced. Peptide maps are the analysis of aprotein sequence in detail to characterize peptide produced following aproteolytic digestion of the conjugated drug product. Once the proteinis digested then the resulting peptides are analyzed by reversed phaseliquid chromatography with mass spectrometry detection (RPLC/MS). Thepresence of conjugate additions on discreet amino acid residues isobserved as a corresponding mass shift compared to the un-conjugatedpeptide. This process has been repeated on multiple antibodiesconjugated with multiple conjugate additions using PFP reactive estersto target lysine residues. (Data is presented below, and also inWO2012007896, whose contents are herein incorporated entirely). In thesestudies, the following observations were consistent: 1—conjugateadditions were observed more frequently on the LC than the HC, 2—CLκ-K⁸⁰is the specific preferred residue that is modified, 3- multiple otherlocations are also modified on both the LC and HC; however, eachalternative site is modified at a low level. To summarize, halo-phenylester conjugation results in preferred modification of CLκ-K⁸⁰ andadditional conjugation is distributed at a low level across multipleresidues. For this reason, the conjugation process is generallyoptimized to result in high % CA values for 2 conjugate additionsbecause this promotes a product that is fully conjugated at a singlelocation on each LC. While elevated % CA levels of 0-1 conjugates resultin preferable CLκ-K⁸⁰ modification, these conjugate forms also representa significant amount of un-reacted scaffold. Products that displayaverage CA values significantly greater than 2 suggest the presence ofconjugate additions that are not targeted at discreet residues. When HCand LC are reduced and analysed separately, the % value of 1 CAindicates the conjugation on single LC species, and is thus reliableindicator of the efficiency of conjugation to the CLκ-K⁸⁰ residue.

Example 1 Exemplary Synthesis of Peptides Used in the Invention

Synthesis of Peptide-Thiol-Linker Compounds

An Ang2-binding peptide (ABP; SEQ ID NO:27) (284 mg, 0.1 mmol) wasdissolved in dimethylformamide (0.5 ml) with stirring. Separately,S-Trityl-mercaptopropionic acid (MPA, 62 mg, approx 0.125 mmol), HBTU(48 mg, 0.125 mmol) and N-methylmorpholine (0.025 ml, 0.25 mmol) werestirred in DMF (0.5 ml) for 5 min until dissolved. The ABP solution andactivated MPA solutions were mixed together for 2 hrs. Progress of thereaction was monitored by LCMS. After 2 hrs, the solution was slowlyadded to ice-cold ether (40 ml) to precipitate the ABP-S-trityl-MPAproduct. The white precipitate was collected by filtration then dried.The solid residue was then dissolved in a solution of trifluoroaceticacid in dichloromethane (1:10, 10 ml), with triisopropylsilane (TIPS)added (0.050 ml) and stirred for 1 hr. The solution was evaporated underreduced pressure to a light-yellow oil then the crude thiol peptideprecipitated by the addition of ice-cold ether. The product wascollected by centrifugation and dried in vacuo. The residue wasdissolved in 50% aqueous acetonitrile then lyophilized to yield thecrude thiol peptide (approx 80% pure by HPLC analysis). The crude thiolpeptide was purified by semi-preparative HPLC to yield 145 mg of SEQ IDNO:27-K_(SH) ¹¹.

Generation of Ang-2-Binding-Peptide-Thiol Intermediates

Peptide chain assembly was conducted on a 0.1 mmol scale. The resin usedwas Fmoc-Rink-PL resin (150 mg, 0.67 mmol/g substitution). Standard Fmocchemistry protocols were used to assemble the peptide. Fmoc removal waswith 20% piperidine/DMF for 3×5 min. and all resin washing steps usedDMF. To incorporate the amino acids, a single coupling step was employedfor each residue, using HBTU/HOBt/NMM activation, for a 2 hr period. TheLinking Residue (K_(SH)) was incorporated asFmoc-Lys(N^(ε)-mercaptopropionate-S-Trt)-OH. Upon chain assembly, theN-terminal Fmoc group was removed and the peptidoresin capped byacetylation. The final resin was washed with DCM and dried overnight invacuo.

Acidolytic removal of protecting groups and cleavage of the peptide fromthe resin was achieved using a cocktail ofTFA/water/dithiothreitol/triisopropylsilane (ratio 90:4:4:2, 5 ml) for 2hrs. The solution was filtered from the resin and the resin washed withanother 5 ml of neat TFA. The combined filtrates were evaporated to asyrup then addition of ice-cold ether precipitated a white powder. Thepowder was collected by centrifugation then dissolved in 50% aqueousacetonitrile (20 ml), frozen and lyophilized overnight.

A preparative HPLC column was pre-equilibrated with dilute aqueous TFAand acetonitrile. The crude ABP-thiol intermediates (i.e. ABP withK_(SH) as linking residue) was dissolved in DMF (3 ml), then adsorbedonto the column and eluted by applying a gradient of acetonitrile indilute TFA. Fractions were collected automatically by mass (M=1465).Elution from the column was monitored by UV, the fractions obtained wereanalyzed by analytical RP-HPLC.

Example 2 Conjugation Strategies

5 different conjugation strategies were considered for conjugatingpeptides to antibodies (exemplary structures are shown using SEQ IDNO:27-K_(SH) ¹¹ and 2.12.1.fx) (full details are provided in theExamples of PCT/US2011/053092, filed 11^(th) Jul. 2011, whose contentsare hereby incorporated entirely). Briefly, NHS esters, maleimide,squarate esters, AZD and halo-phenyl esters were all investigated aspotential mechanisms to develop directional conjugation to antibodies.

NHS esters suffered from the problems of slowly converting to a freeacid form, where the NHS ester is converted to an inactive carboxyl. Itwas concluded that although some success was obtained with NHS esters,it appeared that the aqueous lability of the resulting NHS-ester maylimit their application in subsequent conjugation reactions. Furthertests of NHS-PEG₂-MAL are shown below (comprising Z* group Z13).

The ethyl squarates conjugate well to free thiols but poorly to freeamines on proteins and antibodies unless the pH is above 9.

In general, the maleimide-activated peptides did not conjugate well toproteins or antibodies which lack either an endogenous thiol (derivedfrom a free cysteine side chain) or a thiol introduced by other chemicalmeans, e.g. via Traut's reagent.

AZD reacted slowly with antibody amino groups, and attempts to increasethe pH to 7-9 yielded low levels of conjugation and high levels of AZDhydrolysis (in order to increase the nucleophilic tendency of theantibody surface lysines by decreasing their charge, as the pKa ofsurface lysines is about 9.1 to 11.2).

Example 3 Synthesis of Pentafluorophenyl Esters (PFP)

The present invention also provides for the use of pentafluorophenyl(PFP; Z*═Z1) esters to form relatively stable Effector Moiety-linkercomplexes. This method has several advantages over other approaches inthat the PFP group can be introduced in solution easily from a stableactivated peptide product, which itself can be purified using standardHPLC methods with little PFP ester hydrolysis observed.

The present invention provides a synthetic route whereby an activatedester group, such as PFP, can be coupled directly to a side chain lysineon the peptide by either a chemoselective reaction (usingthiol/maleimide chemistry) or by using a bis-active ester reagent, whichforms an amide with the peptide side chain but leaves the other end asthe active ester.

In some embodiments, the strategy may be a bis-acid PEG with each acidactivated as a PFP ester. In organic solutions, with some base present,the end of the bis-PFP linker reacted with the N-ε-amino side chain oflysine in the required tether position to form a stable amide linkage,while the other end maintained the other PFP group. One potentialproblem with this strategy is the possibility of forming peptide dimers,where a peptide would add to each of the PFP moieties present at eachend of the linker. In some aspects, the present invention overcomes thisadditional problem by altering the stoichiometry and addition of therespective peptide and bis-PEG-PFP linker. One solution provided by theinvention is to have an excess of the bis-Pfp linker in solution andslowly add the peptide in solution, such that an excess of linker overpeptide is always present. By having a ratio of between about 3.7:1 toabout 4.3:1, or in some embodiments, a ratio of about 4:1, of linkerover peptide, the required PFP-activated peptide can be synthesized withno dimer present. The synthesis scheme for [PFP-PEG₅-K¹¹-SEQ:27] isshown below in Scheme 3.

Synthesis of [PFP-PEG₅-K¹¹-SEQ:27]

Bis-dPEG₅-acid (1 mmol, 338 mg) was dissolved in anhydrousdichloromethane (5 ml) then pentafluorophenol (2 mmol, 368 mg) wasadded, along with dicyclohexycarbodiimide (1 mmol, 208 mg). The solutionwas stirred overnight at RT. After this time, the fine whitedicyclohexylurea side-product was filtered off and the filtrateevaporated to dryness to give a pale yellow light oil. Analysis by TLCand HPLC indicated a pure product with correct MS=670. The product wasused in the next step without further purification. The product isstable for several months at −20° C.

SEQ ID NO:27 (730 mg) was dissolved in anhydrous dimethylformamide (8ml) and N-methylmorpholine (0.05 ml) added. An aliquot of neatbis-dPEG₅-OPfp reagent (0.5 ml) was placed in a glass vial (20 ml). Withvigorous stirring, the SEQ ID NO:27/NMM solution was added in 4×2 mlaliquots to the bis-dPEG₅-OPfp reagent over 2 hr, then the final mixturestirred for a further 1 hr. Progress of the conversion to[PFP-PEG₅-K¹¹-SEQ:27] product was monitored by analytical HPLC. At theend of the reaction, the solution was filtered and directly purified bysemi-preparative HPLC on a 1″ C8 column. The purest fractions (>95% byanalytical HPLC) were combined and lyophilized to give 400 mg (48%yield) of final [PFP-PEG₅-K¹¹-SEQ:27] peptide-linker product. A similarmechanism can be used to generate [PFP-PEG₂-MAL-K_(SH) ¹¹-SEQ:27] (seeScheme 4).

Synthesis of [PFP-PEG₂-K_(SH) ¹¹-SEQ:27]

Maleimide-dPEG₂-acid (328 mg, 1 mmol, Quanta Biodesign),pentafluorophenol (0.103 ml, 1 mmol, PFP) and dicyclohexylcarbodiimide(206 mg, 1 mmol, DCC) were dissolved in dry DCM (10 ml) and stirred for1 hr at RT. The fine white precipitate (DCU side-product) that formedwas removed by filtration and the filtrate evaporated to dryness invacuo. The product was obtained as a fine white powder in high yield(490 mg, quantitative). Purity was >95% by analytical HPLC; MS showed[M+H]⁺=495.

A sample (30-40 mg) of SEQ ID NO:27-K_(SH) ¹¹ was dissolved in anhydrousDMF (2 ml). Maleimide-PEG₂-PFP (20 mg) was added along withN-methylmorpholine (5 mL). The reaction was stirred and monitored at RTby HPLC to follow the time-course of product formation. The completeconversion of starting peptide to PFP-activated product was observedwithin the first 2 hrs. The solution was filtered and the product peakdirectly isolated by semi-preparative HPLC. In each case, the productwas isolated in approximately 40% yield after lyophilization.

Example 4 Antibody Conjugation

The MAC-1 and MAC-2 exemplary antibody-Effector Moiety conjugates weremade by conjugating the antibody 2.12.1.fx (SEQ ID NO:1 and SEQ ID NO:2)with an Ang2 binding peptide (SEQ ID NO:27). MAC-1 comprises 2.12.1.fxconjugated to [PFP-PEG₂-MAL-K_(SH) ¹¹-SEQ:27] to yield2.12.1.fx-[PEG₂-MAL-K_(SH) ¹¹-SEQ:27] and MAC-2 comprises 2.12.1.fxconjugated to [PFP-PEG₅-K¹¹-SEQ:27] to yield2.12.1.fx-[PEG₅-K¹¹-SEQ:27].

Generation of MAC-1

Generation of MAC-2

The number of peptide conjugations per 2.12.1.fx antibody in a sample ofeach MAC was calculated (see Table 2).

TABLE 2 Conjugation profile of MAC-1 and MAC-2. Conjugation Additions(CA) (%) 0 1 2 3 4 Avg CA MAC-1 3 26 42 25 3 1.97 MAC-2 2 20 47 26 52.12

Example 5 Optimizing Conditions for PFP-Based Conjugation

A series of assays were run to establish optimal reaction conditions fordirected conjugation. At the end of each reaction conjugation, thereaction was quenched with a succinate and glycine buffer, lowering thepH to approximately 5.5 and quenching any free peptide orpeptide/linker. MAC-2 analysis was conducted by measuring the intactmolecular weight (MW) of the MAC using electrospray time-of-flight massspectrometry detection following protein separation from salts andexcipients through a size exclusion chromatography column.

Temperature

2.12.1.fx antibody was adjusted to 18 mg.ml⁻¹ at pH 7.7 with a phosphatebuffer to a final concentration of 0.06M sodium phosphate.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molarratio of 4.3:1 and allowed to react for 2 hrs at 18, 22, or 25° C.Results are presented in Table 3.

TABLE 3 Reaction temperature in 0.06M phosphate at 4.3:1peptide:antibody. CA (%) Temp 0 1 2 3 4 Avg CA 18 C. 1 16 51 23 8 2.2122 C. 3 15 57 21 5 2.11 25 C. 2 12 53 25 7 2.24

Reaction pH

2.12.1.fx antibody was adjusted to 18 mg.ml⁻¹ at pH 6.5, 6.75, 7.0,7.25, 7.5, 7.75, or 8.0 with a phosphate buffer to a final concentrationof 0.06M sodium phosphate. [PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in apropylene glycol solution to 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was addedto 2.12.1.fx at a molar ratio of 4.3:1 and allowed to react for 2 hrs atRT. The results are presented in Table 4.

TABLE 4 pH in 0.06M sodium phosphate buffer at 4.3:1 peptide:antibody.CA (%) pH 0 1 2 3 4 Avg CA 6.5 7 42 41  9 0 1.51 6.75 3 31 52 12 3 1.837.0 3 24 53 16 4 1.94 7.25 2 18 54 22 5 2.12 7.5 2 12 57 23 7 2.23 7.753 15 55 22 6 2.15 8.0 1 14 52 29 4 2.21

2.12.1.fx was adjusted to 2 mg.ml⁻¹ at pH 7.0, 7.5 and 8.0 with a HEPESbuffer to a final concentration of 0.02M. [PFP-PEG₅-K¹¹-SEQ:27] wasreconstituted in DMSO to 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was added to2.12.1.fx at a molar ratio of 5:1 and allowed to react overnight at RT.The results are presented in Table 5. The level of conjugation decreasedabove pH 8.0

TABLE 5 pH in 0.02M HEPES Buffer at 5:1 peptide:antibody. ABP Additions(%) pH 0 1 2 3 4 Avg CA 7 2 21 41 28 4 2.03 7.5 3 22 44 26 5 2.08 8 9 3042 17 2 1.73

Duration of Conjugation Reaction

2.12.1.fx was adjusted to 18 mg.ml⁻¹ at pH 7.7 with a phosphate bufferto a final concentration of 0.06M sodium phosphate.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molarratio of 4.3:1 and allowed react for 30, 60, 120, 180, 240, 300, or 2400mins at room temperature (Table 6).

TABLE 6 Duration of conjugation reaction in 0.06M sodium phosphate at4.3:1 peptide:antibody. Time CA (%) (mins) 0 1 2 3 4 Avg CA 30 6 38 4413 0 1.64 60 1 22 52 21 3 2.02 120 0 15 50 29 6 2.24 180 1 12 51 31 52.28 240 1 9 51 33 5 2.33 300 1 9 50 35 5 2.35 2400 1 10 48 35 6 2.35

Molar Ratio of Peptide to Protein

2.12.1.fx was adjusted 18 mg.ml⁻¹ to pH 7.5 with a HEPES buffer to afinal concentration of 0.2M HEPES. [PFP-PEG₅-K¹¹-SEQ:27] wasreconstituted in a propylene glycol solution to 10 mg.ml⁻¹.[PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molar ratio of 1, 2,3, 4, and 5:1 (Table 7), and reacted for at least 2 hrs at RT, but thehigh concentration of HEPES buffer resulted in decreased conjugation.

TABLE 7 Molar ratio of peptide to protein 1:1-5:1 in 0.2M HEPES. CA (%)Peptide:2.12.1.fx 0 1 2 3 4 5 6 7 Avg CA 1:1 80 20 0 0 0 0 0 0 0.20 2:160 35 5 0 0 0 0 0 0.45 3:1 39 49 12 0 0 0 0 0 0.73 4:1 27 51 19 3 0 0 00 0.98 5:1 11 47 37 5 0 0 0 0 1.36

2.12.1.fx was adjusted 18 mg.ml⁻¹ to pH 7.7 with a phosphate buffer to afinal concentration of 0.06M sodium phosphate. [PFP-PEG₅-K¹¹-SEQ:27] wasreconstituted in a propylene glycol solution to 10 mg.ml⁻¹.[PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molar ratio of 5, 7,10, 12, and 15:1 (Table 8) and allowed to react for 2 hrs at RT togenerate a MAC with a higher level of conjugation.

TABLE 8 Molar ratio of peptide to protein 7:1-15:1 in 0.06M sodiumphosphate. CA (%) Peptide:2.12.1.fx 0 1 2 3 4 5 6 7 Avg CA  7:1 1 1 2939 17 10 2 0 3.06 10:1 1 1 18 33 25 19 3 0 3.49 12:1 3 1 11 22 26 26 8 33.92 15:1 1 2 9 19 23 32 12 3 4.22

To further optimize the molar ratio of 2.12.1.fx and[PFP-PEG₅-K¹¹-SEQ:27], 2.12.1.fx was adjusted 18 mg.ml⁻¹ to pH 7.7 witha phosphate buffer to a final concentration of 0.06 M sodium phosphate.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx antibody ata molar ratio of 2.5, 2.8, 3.1, 3.4, 3.7, 4.0, 4.3, or 4.6:1 (Table 9)and allowed to react for 2 hrs at RT.

TABLE 9 Molar ratio of peptide to protein 2.5:1- 4.6:1 in 0.06M sodiumphosphate. CA (%) Peptide:2.12.1.fx 0 1 2 3 4 5 6 7 Avg CA 2.5:1 14 5330 4 0 0 0 0 1.25 2.8:1 10 45 37 8 0 0 0 0 1.43 3.1:1 7 39 45 8 0 0 0 01.53 3.4:1 5 40 44 11 0 0 0 0 1.61 3.7:1 4 25 51 15 5 0 0 0 1.92 4.0:1 226 55 15 2 0 0 0 1.89 4.3:1 1 24 55 16 4 0 0 0 1.98 4.6:1 2 19 56 19 5 00 0 2.08

2.12.1.fx was adjusted to 2 mg.ml⁻¹ at pH 7.0 with a HEPES buffer to afinal concentration of 0.02M. [PFP-PEG₅-K¹¹-SEQ:27] was reconstituted inDMSO to 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at amolar ratio of 5, 6, 7, 8, 10:1 and allowed to react overnight at RT.The results are presented in Table 10.

TABLE 10 Molar ratio of peptide to protein 5:1-10:1 in 0.02M HEPES. CA(%) Peptide:2.12.1.fx 0 1 2 3 4 5 6 7 Avg CA  5:1 2 21 49 24 4 0 0 02.07  6:1 2 15 42 32 9 0 0 0 2.31  7:1 1 11 34 42 13 0 0 0 2.57  8:1 0 932 42 16 1 0 0 2.68 10:1 0 4 21 47 25 4 0 0 3.07

Conjugation Profile of 2.12.1.fx at Various Protein Concentrations

The conjugation profiles of 2.12.1.fx with [PFP-PEG₅-K¹¹-SEQ:27] atvarious concentrations were analyzed. 2.12.1.fx was concentrated to >50mg/mL, diluted to the desired concentration with 20 mM sodium acetate,200 mM trehalose pH 5.5, and spiked with 60 mM sodium phosphate pH 7.7.[PFP-PEG₅-K¹¹-SEQ:27] was resuspended with 50% propylene glycol andmixed with the antibody at a 4.3:1 molar ratio and allowed to reactovernight at RT. All samples were diluted to 2 mg/ml and analyzed as anintact conjugated protein by size exclusion chromatography-massspectrometry (SEC-MS) to determine the number and quantitation ofconjugate forms of the protein. This technique measures the molecularweight of each protein form; multiple conjugation sites are observed asdistinct signals separated by the mass difference of a peptide. Relativequantitation of multiple conjugation species is performed by measuringthe signal magnitude. Table 11 shows the conjugation profile of2.12.1.fx with peptide at various concentrations of antibody. Atantibody concentrations 10 mg/mL to 50 mg/mL, the conjugation occurs ata distribution between 0-5 addition with an average of 1.8 or greateradditions. At antibody concentrations 0.5 to 5 mg/mL, the conjugationoccurs at a distribution between 0-3 additions with an average of 1.5 orless additions.

TABLE 11 Effect of antibody concentration. Antibody Concentration CA (%)(mg/ml) 0 1 2 3 4 5 Avg CA 0.5 65 32 3 — — — 0.37 1 44 44 12 — — — 0.675 10 41 40 8 — — 1.45 10 3 30 47 17 2 1 1.87 15 1 24 51 20 3 1 2.02 20 116 57 22 2 1 2.11 30 2 20 55 20 3 1 2.04 40 2 21 53 22 2 0 2.04 50 2 1950 24 4 1 2.11

Reaction Buffer Selection

2.12.1.fx was adjusted to 18 mg.ml⁻¹ at pH 7.7 with a sodium carbonate,sodium borate, or sodium phosphate buffer to a final concentration of0.05M sodium phosphate. [PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in apropylene glycol solution to 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was addedto 2.12.1.fx at a molar ratio of 1, 2, 3, 4, or 5:1 and allowed to reactfor 2 hrs at RT. The low reaction pH resulted in the reduced level ofconjugation (Table 12).

TABLE 12 Buffer and pH alterations. CA (%) Buffer 0 1 2 3 4 Avg CA 50 mMsodium carbonate pH 7.4 2 24 48 26 0 1.98 50 mM sodium borate pH 7.0 117 45 31 5 2.20 50 mM sodium phosphate pH 7.0 10 48 38 4 0 1.36

2.12.1.fx was adjusted to 18 mg.ml⁻¹ at pH 7.5, 7.7 and 8.0 with asodium borate and sodium phosphate buffer to a final concentration of0.04 M. [PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycolsolution to 10 mg.ml⁻¹ and added to 2.12.1.fx at a molar ratio of 4.3:1,and reacted for 2 hrs at RT (Table 13).

TABLE 13 Buffer and pH alterations. CA (%) Buffer 0 1 2 3 4 Avg CAPhosphate, pH 7.5 1 21 53 21 3 2.02 Phosphate, pH 7.7 0 15 50 29 6 2.26Phosphate, pH 8.0 1 14 52 29 4 2.21 Borate, pH 7.5 46 44 10 0 0 0.64Borate, pH 7.7 22 51 23 4 0 1.09 Borate, pH 8.0 1 17 48 30 4 2.19

2.12.1.fx was adjusted to 18 mg.ml⁻¹ at pH 7.7 with a phosphate bufferto a final concentration of 0.04 M, 0.06 M, or 0.08 M sodium phosphate.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molarratio of 4.3:1 and allowed to react for 2 hrs at RT. The results arepresented in Table 14.

TABLE 14 Concentration of phosphate. Concentration (mM) of CA (%)phosphate at pH 7.7 0 1 2 3 4 Avg CA 40 2 23 54 16 4 1.95 60 2 28 51 154 1.91 80 2 29 51 13 4 1.86

Effect of Buffer Constituents on Conjugation

Propylene Glycol:

2.12.1.fx was adjusted to 18 mg.ml⁻¹ at pH 7.7 with a phosphate bufferto a final concentration of 0.06 M sodium phosphate.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 20 mg.ml⁻¹ (5% propylene glycol in the conjugation reaction).[PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molar ratio of 4.3:1and spiked with an additional 0 to 15% propylene glycol (final propyleneglycol percentage of 5, 10, 15, and 20%) and allowed to react for 2 hrsat RT. The results are presented in Table 15.

TABLE 15 Percent of propylene glycol in 0.06M sodium phosphate. CA (%)Percent (%) Propylene Glycol 0 1 2 3 4 Avg CA 5 2 18 55 20 5 2.08 10 220 53 21 5 2.09 15 2 23 49 20 5 2.01 20 4 23 50 19 4 1.96

NaCl:

2.12.1.fx was adjusted to 2 mg.ml⁻¹ at pH 7.0 with a HEPES buffer to afinal concentration of 0.02M in the presence and absence of 0.14M NaCl.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in DMSO to 10 mg.ml⁻¹.[PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molar ratio of 5:1 andallowed to react overnight at RT. The level of conjugation decreases inthe presence of NaCl (Table 16).

TABLE 16 Concentration of sodium chloride in 0.02M HEPES. Concentrationof sodium ABP Additions (%) chloride (mM) 0 1 2 3 4 Avg CA 0 2 21 41 284 2.03 0.14 9 34 42 14 1 1.64

HEPES:

2.12.1.fx was adjusted to 2 mg.ml⁻¹ at pH 7.0 with a HEPES buffer to afinal concentration of 0.2 M and 0.02 M. [PFP-PEG₅-K¹¹-SEQ:27] wasreconstituted in 50% propylene glycol to 10 mg.ml⁻¹.[PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx at a molar ratio of 5:1 andallowed to react 2 hrs at RT. The results are presented in Table 17. Thelevel of conjugation is reduced at 0.2M HEPES buffer.

TABLE 17 HEPES concentration. ABP Additions (%) Concentration of HEPES(mM) 0 1 2 3 4 Avg CA 0.02 2 35 47 16 0 1.77 0.2 21 49 26 4 0 1.13

DMSO:

2.12.1.fx was adjusted to 15 mg.ml⁻¹ at pH 7.7 with sodium phosphatebuffer to a final concentration of 0.06 M and DMSO was added to a finalconcentration of 30%. [PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in apropylene glycol solution to 10 mg.ml⁻¹. [PFP-PEG₅-K¹¹-SEQ:27] was addedto 2.12.1.fx at a molar ratio of 4:1 and allowed to react for 2 hrs atRT. The results are presented in Table 18.

TABLE 18 DMSO in 0.06M sodium phosphate. ABP Additions (%) Percent ofDMSO 0 1 2 3 4 Avg CA 0 3 28 49 14 6 1.92 30 8 28 32 22 10 1.98

Discussion of Conjugation Reaction Parameters

When the molar ratio of Effector Moiety (in this example, a peptide) toantibody is reduced below about 3.5:1, the level of conjugation isdecreased, as seen in Table 9. Alternatively, Table 10 shows thatincreasing the molar ratio results in an increased level of conjugation.Increasing the number of peptides per antibody generally decreases thebinding efficiency of the antibody (in this case 2.12.1 fx) to itsantigen (in this case the IGF1R receptor), therefore the molar ratio ofpeptide to antibody was optimized to maximise both antibody-antigen, andpeptide-cognate binding.

It was also found that varying the conjugation buffer can alter theconjugation pattern. Amine-containing excipients are less preferable ingeneral as they can react with the PFP group. Buffers such as carbonateand borate can be used for conjugation but were avoided as their pKa(boric acid with a pKa ˜9 and carbonate with two pKa of ˜6 and ˜11) werefar from the conjugation pH of 7.7 that was identified as optimal forMAC-1 and MAC-2 (Table 12). The level of conjugation is not onlydependent on the chemical conditions of the reaction but also based ontime. After 2 hrs, most of the PFP-activated peptide had reacted withthe antibody or the PFP Z* has hydrolyzed (Table 6).

The PFP-activated peptide/linker reacted quickly with lysine side chainamino groups. Conjugation was performed at pH 6.5 to 8 in phosphatebuffer to increase the nucleophilic tendency of the antibody surfacelysines by decreasing their charge (the pKa of lysines on the surfaceproteins is about 9.1 to 11.2) as shown in Tables 4 and 5.

Optimal conditions for conjugation of MAC-1 and MAC-2 are described asfollows: 2.12.1.fx antibody was adjusted to pH 7.7 with a phosphatebuffer to a final concentration of 0.06M sodium phosphate.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 10 mg.ml⁻¹ (final propylene glycol concentration in reaction is 10%).[PFP-PEG₅-K¹¹-SEQ:27] was added to 2.12.1.fx antibody at a molar ratioof 4.3:1 and allowed to react for 2 hrs at RT. The reaction was quenchedwith a succinate and glycine buffer, lowering the pH to approximately6.0 and quenching any free peptide. In some aspects, the reaction may beconcentrated and peptide-related species (such as peptides where thelinker was hydrolyzed by reaction with water solvent) and other elementsof the reaction mixture (such as PFP) may be removed by diafiltration,for example, using a 50 kDa membrane or size exclusion chromatographyinto a succinate, glycine, sodium chloride, and trehalose buffer, pH 5.5at 30 mg/ml.

The conjugation conditions listed above were varied to determine therange of each process parameter. Parameter ranges were set based onvariability that may occur during the conjugation and/or were expandeduntil greater than 10% change in species population was observed. Table19 summarizes the parameters that result in similar conjugation profilesfor MAC-2.

TABLE 19 Process parameters optimized for MAC-2. Parameters tested Rangetested Desirable range Optimum Temperature 18-25° C. 18-25° C. RTReaction pH 6.5 to 8.0 pH 7.25-8.0 7.7 Reaction duration 30-2400 mins180-2400 mins >about 2 hrs Molar ratio of Peptide to Antibody 2.5 to 4.63.7:1 to 4.3:1 4.3:1 2.12.1.fx concentration added to the reaction 0.5to 50 mg/mL 10 to 50 mg/mL 20 mg/mL Phosphate concentration in thereaction buffer 40 to 80 mM 40-80 mM 60 mM Final propylene glycolconcentration 5 to 20% 5-20% 10 %

Example 6 Location of Conjugated Peptides on Antibody

The MAC-2 drug product molecule consists of a distribution of 1-4[PEG₅-K¹¹-SEQ:27] molecules attached to the 2.12.1.fx antibody. This wasdetermined by measuring the intact molecular weight (MW) of MAC-2 usingelectrospray, time-of-flight mass spectrometry detection followingprotein separation from salts and excipients through a size exclusionchromatography column. Mass spectrometry data that demonstrated the MWof the 2.12.1.fx and 3 lots of MAC-2 are shown in FIG. 2. FIG. 1A shows2.12.1.fx before conjugation. This is a uniform molecule that displays asingle MW. The MAC-2 lots display a distribution of conjugated peptidesto 2.12.1.fx; between 1-4 conjugation additions (CA) are observed. Therelative amount of each form is consistent between lots and the mostcommon form in each lot has 2 peptides (SEQ ID NO:27) attached to eachindividual 2.12.1.fx antibody.

By reducing disulfide bonds in the 2.12.1.fx antibody, light and heavychains are observed separately. Disulfide reduction is performed bytreating the intact 2.12.1.fx antibody with 20 mMtris(2-carboxyethyl)phosphine (TCEP). The resulting mixture of heavy andlight chains is analyzed for intact molecular weight as described above.The data shown in FIG. 2 provides evidence toward the location of theABP on 2.12.1.fx. The majority of light chain (>65%) in the MAC-2 lotsare conjugated. Most of the conjugated light chain contains 1CA. 2CA isalso observed at a lower level. Almost all observed heavy chain (>90%)is unmodified, which suggests that very few of the conjugated peptidesare located on the heavy chain.

Peptide mapping was used to determine the precise location ofconjugation. The procedure was as follows: an aliquot of MAC-2 wasdenatured with 8M Guanidine-hydrochloride, disulfide bonds were reducedwith TCEP, and the resulting cysteine sulphydryls were alkylated withIodoacetamide. This treated protein sample was then digested with theprotease chymotrypsin (1:125 protease:MAC ratio by weight). Theresulting chymotryptic peptides were then detected individually by massspectrometry after separation through a C8 liquid chromatography column.With this technique, MAC-2 was digested by chymotrypsin on the heavy andlight chains into fragments at the locations noted in the sequence (withbullets) in FIG. 3. Liquid chromatography-mass spectrometry (LC-MS)detection of the MW of each peptide was then used to determine whichLysine residues are modified by a conjugated peptide. If a fragment wasmodified by attachment of conjugated peptide, its MW was shiftedaccordingly.

Fragments Y1, Y6, Y9, Y10, Y20, Y25, Y26, Y29, Y32, Y33, Y34, Y37, Y40and Y43 of the heavy chain contain Lys residues. Of these, peptideconjugation was detected at Y6, Y10, Y25, Y33, and Y37. Fragments Y3,Y10, Y11, Y12, Y13, Y14, Y15, and Y16 of the light chain contain Lysresidues. Of these, conjugation was detected at Y3, Y13, and Y15.

The light chain fragment referred to as Y15 (the 15^(th) chymotrypticfragment on the light chain from the N-terminus) was found to beconjugated based on the data shown in FIG. 4. The MW of the modified Y15fragment in MAC was clearly detected. In the un-conjugated 2.12.1.fxsample, there was no evidence of modified Y15 fragment. The unmodifiedY15 fragment was observed in both MAC-2 and 2.12.1.fx. The magnitude ofthis fragment is higher in the 2.12.1.fx sample because this entirefragment is present in the un-modified form. As this fragment isconjugated in MAC-2, the observed level of un-modified Y15 decreases,which is seen in FIG. 4 as a peak with a smaller area.

The amount of conjugation of [SEQ:27-K¹¹-PEG5] observed on light chainfragment Y15 in MAC-2 is estimated by measuring the decreased peak areaof un-modified Y15. After normalizing the signal intensity such thatunconjugated 2.12.1.fx showed 100%, 3 independent lots of MAC-2 showed17%, 27% and 22% unconjugated Y15 fragments respectively.

The observed magnitude of Y15 in the MAC samples was normalized to themagnitude of Y15 in the 2.12.1.fx sample. Between 75-85% of the Y15fragments are determined as modified in MAC-2. Considering that MAC-2contains mostly 1-2 conjugation additions, this suggests that most ofthe conjugation in MAC-2 is located at one of the 2 K residues of lightchain fragment Y15 (LC-K¹⁸⁸ or LC-K¹⁹⁰). The location of fragment Y15 inrelation to the sequence of 2.12.1.fx is shown in FIG. 3.

Trypsin enzymatic digestion was used to discriminate between LC-K¹⁸⁸ andLC-K¹⁹⁰ (trypsin has specificity for the C-terminus of K and R). Astrypsin does not digest conjugated K residues, the enzymatic digestiongenerates different peptide lengths, depending on which K residue isconjugated. Examination of LCMS data from MAC-2 that was digested withtrypsin provides evidence that the peptide attaches specifically toLC-K¹⁸⁸. No evidence of modified LC-K¹⁹⁰ was observed.

MAC-2 was reduced with TCEP and denatured with guanidine hydrochlorideas described above. The protein concentration was adjusted to 2 mg/mland the pH to 7.8 with Tris digestion buffer. Purified trypsin was addedat a 1:125 protease:MAC ratio by weight and incubated at 30° C. for 4hrs. Samples were stored at −20° C. until analyzed by LCMS. Fragmentsamples were separated on a C18 reversed phase column usingwater/acetonitrile+0.1% TFA mobile phases. Detection of fragments wasmonitored both by UV 214 nm and ESI-TOF mass spectrometry. All dataanalysis was performed using MassLynx software.

The formation of fragments upon trypsin digestion of MAC-2 depends onthe site of peptide conjugation. Lysines are the targeted residue forconjugation. Data shown in FIGS. 1-4 indicates that the predominant siteof peptide binding is either LC-K¹⁸⁸ or LC-K¹⁹⁰. The scheme below showsthe trypsin digestion reactions that would occur upon conjugation ateither 2.12.1.fx-[LC-K¹⁸⁸] or 2.12.1.fx-[LC-K¹⁹⁰].

The chemical structures of the two potential digestion fragments inquestion are as follows:

FIG. 5 shows the selected ion LCMS chromatogram data for the trypsinpeptide when LC-K¹⁸⁸ is conjugated to the peptide. FIG. 6 shows theselected ion LCMS chromatogram data for the trypsin fragment whenLC-K¹⁹⁰ is modified with a conjugated peptide. These data suggest thatonly LC-K¹⁸⁸ alone is conjugated; this situation results in asignificant signal that is detected in MAC-2 but is absent in the2.12.1.fx control experiment. The results from modification at LC-K¹⁹⁰do not provide any data that is unique compared to the negative control.

In contrast to what may be expected, the peptide/linker appears topreferentially decorate LC-K¹⁸⁸ of the light chain of 2.12.1.fx. Thishas the surprising advantage that the Fc portion of the 2.12.1.fxantibody is unaffected. Tests show that the resulting PK of MAC-2 isapproximately equal to the PK of unconjugated 2.12.1.fx. Promiscuous,non-specific conjugation to multiple sites on an antibody can result ina product with lower PK. The directional conjugation of the invention,exemplified by MAC-1 and MAC-2, provide the advantage of minimizing someof the possible deleterious effects that can be caused by promiscuous,non-specific conjugation, including lower PK. LC-K¹⁸⁸ is the sameresidue as CLκ-K⁸⁰ (i.e. K⁸⁰ of SEQ ID NO:6), as the Light Chain (LC)comprises the variable region as well as the constant light kappa chain(CLκ).

To establish the reproducibility of the process, the experiment wasrepeated. MAC-2 was diluted to 2 mg/ml and analyzed as an intactconjugated protein by size exclusion chromatography-mass spectrometry(SEC-MS) to determine the number and quantitation of conjugate forms ofthe protein. This technique measures the molecular weight of eachprotein form; multiple conjugation sites are observed as distinctsignals separated by the mass difference of a conjugated peptide/linker.Relative quantitation of multiple conjugation species is performed bymeasuring the signal magnitude. FIG. 7A shows a representative spectrumof MAC-2; the calculations used for quantitation are shown in Table 20.The average conjugation addition for the intact MAC-2 is calculated as2.11 using the following formula: SUMPRODUCT (Number of ConjugationAdditions (CA), Percent per CA). This example demonstrates conjugationof peptides occurring as a distribution between 0-4 peptide additionswith the largest form being 2 peptide additions and the average numberof peptide additions is 2.11. Replicate analysis by multiple individualsdemonstrates that the profile of conjugation is consistent andreproducible.

TABLE 20 Weighted average of conjugation additions: 2.11. Conjugationadditions Predicted mass Intensity Percent 0 149210 1615  1% 1 15235020533  17% 2 155490 69395  56% 3 158630 27708  22% 4 161770 4818  4%124069 100%

The extent of peptide conjugation was examined separately on the lightand heavy chains of 2.12.1.fx. MAC-2 was denatured and disulfide bondswere reduced using guanidine hydrochloride and dithiothreitol. Theresulting free light and heavy chains were analyzed using LCMS todetermine the conjugation profile on each. FIGS. 7B and 7C show arepresentative spectrum of each chain; the calculation used forquantitation are shown in Table 21. The average conjugation additions(Avg CA) for the reduced heavy chain MAC-2 is calculated as 0.14 and theAvg CA for the reduced light chain MAC-2 is calculated at 0.86 using thefollowing formula: SUMPRODUCT (Number of Conjugation Additions (CA),Percent per CA). These data demonstrate that the location of conjugationis higher on the light chain; the most abundant form on the light chaincontains one peptide addition and the light chain contains an average of0.86 peptide additions. Conjugation on the heavy chain is observed at asignificantly lower level. Replicate analysis of this experiment bymultiple individuals demonstrates that the profile of conjugation isconsistent and reproducible.

TABLE 21 Peptide mapping characterization of MAC-2 identifying specificlocation of conjugation. Mass Conj. (Da) Additions Species IntensityPercent Avg CA 51020 0 HC 102093  86% 54165 1 HC + (1×) ABP-1 16204  14%Total HC 118297 100% 0.14 23584 0 LC 19752  21% 26729 1 LC + (1×) ABP-168757  72% 29874 2 LC + (2×) ABP-2 6561  7% Total LC 95070 100% 0.86

MAC-2 was reduced with dithiothreitol and cysteine residues werealkylated by carboxymethylation with iodoacetamide. Chymotrypsin wasused for proteolytic digestion. Digested fragments in solution wereanalyzed using liquid chromatography mass spectrometry (LCMS).Individual fragments were separated over a C18 HPLC column and theiraccurate mass is measured in a Quadrupole Time-of-Flight (Q-ToF) massspectrometer. The resulting fragment mass was used to identifyunmodified fragments or fragments modified with a conjugated peptide.This experiment was interpreted by focusing on chymotryptic fragmentsthat contain a lysine residue, as these were possible sites for peptideconjugation. Table 22 shows a listing of all such fragments. Blankentries are fragments that are not detected using this technique.Detected fragments that are observed with a peptide modifier areconsidered potential sites of conjugation.

The table entries for Table 17 are explained below:Fragment number: Chymotrypsin fragment numbering from the N-terminus;joined fragments (i.e. Y1-2) indicate a missed cleavage site.Start/End: Numbering of the fragment location from the N-terminus.Peptide Mass (Da): Theoretical mass of the fragment listed in Daltons.Retention Time (Control/Analyte): Time of chromatographicretention/elution in the LCMS fragment mapping experiment.MS Signal Intensity (Control/Analyte): Magnitude of observed signalobserved by MS.Mass Error- ppm (Control/Analyte): Comparison of theoretical vs.observed mass of the fragment; values >10, and especially closer to zero(0) demonstrate better mass accuracy.Modifiers: Potential covalent additions to the fragment;peptide-antibody binding fragment of Lys residue, CAM-carboxymethylation of Cysteine residue.Asterisks indicate the modified (e.g. conjugated) version of therespective fragment. Pep indicates a conjugated peptide.

Directional conjugation of a peptide to the Y15 fragment is demonstratedby quantitating the conjugation level. The following analysis wasperformed on each of the peptide fragments that were observed havingconjugation during the peptide mapping experiment of the 2.12.1.fxreference product. The ratio of observed signal intensity for theunmodified peptide in the non-conjugated control (2.12.1.fx antibodyscaffold—no conjugation) compared to the conjugated reference product(MAC-2) is shown in Table 23. The unmodified signal is used because adirect comparison of the same peptide signal is possible in each sample.For example, an unconjugated peptide would be expected to have the sameobserved signal intensity in the control vs. product samples resultingin a ratio of one (1). Conjugation would result in a decrease in theobserved amount of unmodified peptide in the product sample which wouldbe indicated by a ratio greater than one (1). The data in Table 23 wasfurther normalized to correct for sample and experimental variationbetween the control and product. Table 23 demonstrates that light chainpeptide Y15 is conjugated at a significantly higher level than each ofthe other conjugated peptides. This suggests that conjugation occurs ina directional manner and is not randomly distributed across K residues.

TABLE 22 Peptide mapping characterization of MAC-2 heavy chain referenceproduct. Peptide Fragment Mass Retention Time MS Signal Intensity MassError (ppm) Number Start End (Da) Control Analyte Control AnalyteControl Analyte Modifiers Y1 1 27 2617.3533 Y1-2 1 29 2865.4695 Y5-6 3447 1657.8398 Y6 37 47 1253.688 19.2 19.2 516640 583534 1.9 −1.1 Y6-7 3750 1602.8518 22.1 22.1 26537 37988 −1.6 −2.2 Y6-7* 37 50 3295.7017 21.86316 −19.4 Pep(1) Y8-9 51 68 1931.9337 16.5 16.5 60894 85742 −2.2 0.4 Y961 68 878.461 11.3 11.3 376224 412997 0 −1 Y9-10 61 80 2241.1501 Y10 6980 1380.6997 13.3 13.3 261813 299847 −1.1 0.7 Y10* 69 80 3073.5498 23.46350 −8.7 Pep (1) Y10-011 69 94 2972.4661 Y19-20 111 157 4748.2773 Y20116 157 4160.0405 Y20-21 116 166 5202.5527 Y20-21* 116 166 5316.595734.1 6445 0.5 CAM(2) Y24-25 202 245 4702.2109 Y25 207 245 4151.9722 Y25*207 245 4437.0796 20.9 20.9 1495322 1800079 1.1 −3.1 CAM(5) Y25* 207 2456129.9297 24.4 6652 −4.5 CAM(5) Pep(1) Y25-26 207 279 7985.9092 Y26 246279 3851.9478 Y26-27 246 281 4152.0698 Y28-29 282 300 2245.1128 Y29 283300 2082.0493 14.6 14.6 20665 16662 −0.6 −3.8 Y29-30 283 304 2531.2405Y31-32 305 323 2241.1907 Y32 318 323 722.3599 7.9 7.9 93966 96639 0.12.6 Y32 318 323 722.3599 17.7 18.4 37943 12802 11.4 30.6 Y32 318 323722.3599 18.4 11761 23.8 Y32-33 318 353 4028.188 Y33 324 353 3323.838620 5422 3.1 Y33* 324 353 3380.8601 19.7 19.7 2196329 2497507 −2.5 −3.1CAM(1) Y33* 324 353 5073.71 24 5973 1.3 CAM(1) Pep(1) Y33-34 324 3765883.1577 Y34 354 376 2577.3293 Y34-35 354 385 3637.8159 Y34-35* 354 3853694.8374 33 32.9 10095 20682 1.9 −2.4 CAM(1) Y36-37 386 408 2527.0808Y37 396 408 1394.6388 19.6 19.6 62942 71902 −0.9 −0.4 Y37-38 396 4091541.7072 25.1 25.1 827336 878570 0 −1.9 Y37-38* 396 409 3234.5571 29.77749 −5.3 Pep(1) Y39-40 410 421 1494.8195 Y40 412 421 1218.672 15.8 15.877917 88243 −0.3 −1.6 Y40-41 412 427 1891.9905 20.3 20.3 107513 1496760.2 −2 Y42-43 428 450 2525.1792 Y43 441 450 1016.5502 Y2-3 36 491688.9725 16.2 16.2 145374 170451 −1.7 −2.6 Y2-3* 36 49 3381.8225 24.27192 −9.2 Pep(1) Y3 37 49 1525.9093 15.5 15.5 331068 393638 −2.7 −2.9Y3* 37 49 3218.7593 24 28193 −9 Pep(1) Y3-4 37 62 2882.6355 Y9-10 88 1163244.729 Y10 99 116 1871.0992 Y10-11 99 139 4331.335 Y11 117 1392478.2463 22.8 47035 −5.9 Y11-12 117 148 3635.8445 Y12 140 148 1175.6088Y12-13 140 173 3886.8245 Y13 149 173 2729.2263 13.1 13.1 1140556 1218022−1.1 0.1 Y13* 149 173 4422.0762 21.4 8424 −6.5 Pep(1) Y13-14 149 1864095.9243 Y14 174 186 1384.7086 Y14-15 174 192 2169.1318 Y15 187 192802.4337 7.5 7.5 275639 62720 −1.9 −0.2 Y15* 187 192 2495.2837 20.9936267 −9.8 Pep(1) Y15-16 187 209 2574.29 Y16 193 209 1789.8668 18.75400 4.4 Y16* 193 209 1846.8883 18.1 18.1 169490 235914 −1.7 −2.5 CAM(1)Y16-17 193 214 2349.0842 17.8 9211 0.1

TABLE 23 Directional conjugation of peptide to Y15 fragment on the lightchain. Unmodified Intensity Ratio: Control/Analyte- Fragment normalizedLight Y3  1.000 Light Y13 1.112 Light Y15 5.218 Heavy Y6  0.831 HeavyY10 1.038 Heavy Y25 0.988 Heavy Y33 1.045 Heavy Y37 1.120

Example 7 Demonstration of Potency of MAC Products

Full details of in vitro and in vivo assays of MAC-1 and MAC-2 areprovided in the Examples of PCT/US2011/053092 (WO2012/007896).Ang2-h38C2-IgG1 was used as a control in certain examples. Thegeneration and structure of the Ang2-h38C2 is fully described ascompound 43 in WO2008056346, whose contents is incorporated herein, withparticular reference to aspects referring to the generation of compound43. Briefly, the structure is as follows:

wherein the linker is covalently attached to the ε-amino group of HC-K⁹⁹(K⁹³ according to Kabat numbering) of the combining site of the antibodyand the antibody is h38C2-IgG1 (SEQ ID NO:64 and 65) (SEQ ID NO:189 andSEQ ID NO:190 of WO2008/056346).

In summary, MAC-1 and MAC-2 were able to bind Ang2 and prevent itsbinding to Tie2 as shown in an Ang2 competition assay, and both MAC-1and MAC-2 have similar activity as the parental anti-IGF1R antibody(2.12.1.fx) for competing with IGF1 for IGF1R binding (Table 24).Surprisingly, in comparison with Ang2-h38c2, MAC-1 and MAC-2 both showedan increase in ability to competitively bind Ang2. Therefore,conjugation of limited Ang2 peptides does not appear to change theinnate binding and inhibition of the antibody, and may in some casesimprove the Effector Moiety activity.

The MACs were tested for the ability to downregulate IGF1R levels on ahuman colon carcinoma cell line Colo205. Cells were treated for 3 hrs inculture with titration of MAC compounds. Cells were collected and IGF1Rsurface expression determined by flow cytometry. The percentage of IGF1Rdownregulated as compared to negative control hIgG2 was determined(Table 23).

TABLE 24 Ability of MAC-1 and MAC-2 to bind & modulate IGF1R and Ang2.IGF1R Ang2 IGF1R phosphorylation % IGF1R IC₅₀ (nM) IC₅₀ (nM) IC₅₀ (nM)downregulated MAC-1 0.092 ± 0.049 5.1 ± 1.1 150.7 ± 59.6 43 ± 5 MAC-20.057 ± 0.022 6.1 ± 1.1  91.4 ± 40.2 50 ± 5 2.12.1.fx nd 3.8 ± 0.8  48.7± 14.0 48 ± 3 antibody Ang2-h38c2- 0.582 ± 0.242 nd nd nd IgG1

It was also demonstrated that conjugating 2 peptides per antibody wasideal in terms of effecting IGF1R autophosphorylation and downregulationand that conjugating more or less than 2 peptides per antibody lessensthe ability of the MAC to effect these functions.

To assess the effect of the number of peptides per antibody on theability of 2.12.1.fx to modulate IGF1R activity, 2 samples of MAC-1 wereprepared where the reaction conditions were set to provide eitherreduced conjugation (MAC-1 low) or increased conjugation (MAC-1 high)(Table 25). The samples were analysed for the ability to downregulateand phosphorylate IGF1R (Table 25). There is a significant difference inthe ability of the MAC-1 high as compared with MAC-1 low to effectivelymodulate the IGF1R pathway. Conjugation of greater than about 2 peptidesper antibody limits the functional activity of the MAC to both inhibitIGF1R auto-phosphorylation and induce IGF1R downregulation, compared toconjugation of about 2 or less peptides per antibody. Therefore, inorder to efficiently modulate 2 different biological pathways in onebifunctional entity, conjugation of about 2 peptides per antibody may beideal (depending on peptide's and target's pharmacokinetic profile).

TABLE 25 Analysis of MAC-1-High and MAC-1 Low. Ang2 Phosphorylation IC₅₀% IGF1R IGF1R IC₅₀ CA (%) Avg (nM) downregulated (nM) 0 1 2 3 4 5 CAMAC-1 Low 0.103 32 ± 1 12.8 14 42 32 12 0 0 1.42 MAC-1 High 0.035  9 ±2 >300 0 4 19 41 32 5 3.18 2.12.1.fx nd 36 ± 3 3.5 Ang2- 0.252 nd ndh38c2-IgG1

Example 8 In Vivo Pharmacokinetics

PK studies were conducted using male Swiss Webster mice and 2 maleCynomolgus monkeys (Macaca fascicularis). Full details of PK studies areprovided in the Examples of PCT/US2011/053092. In mouse, MAC-1 and MAC-2demonstrated similar residence time as the parental anti-IGF1R antibodywith β phase half-lives of 383-397 hrs. The MAC-1 and MAC-2 Ang2 bindingcapability demonstrated similar residence time as Ang2-h38c2 with T½ of105-120 hrs in mouse in single dose IV studies. In cynomolgus monkey,MAC-2 demonstrated a slightly shorter residence time as the parentalanti-IGF1R antibody with T½ of 100.4 hrs. The MAC-2 Ang2 bindingcapability demonstrated similar residence time as Ang2-h38c2 with T½ of97.8 hrs.

TABLE 26 Single-dose PK of IV administered MACs at 10 mg/mkg in mouseand cynomolgus monkey. α-IGF1R antibody dosed at 10 mg/kg in mouse, and5 mg/kg in monkey. Mouse β-T ½ (hr) Monkey T ½ (hr) Compound (mg · Kg⁻¹)Ang2 IGF1R Ang2 IGF1R Ang2-h38c2, (10) 95.2 — 95.3 — α-IGF1R antibody,(10), (5) — 390 — 146.4 MAC-1, (10) 105 383 NT NT MAC-2, (10) 120 39797.8 100.4 NT: not tested.

Example 9 In Vivo Pharmacology

The anti-tumour activity of MAC-2 was evaluated in the Colo205 (humancolon adenocarcinoma) or MDA-MB-435 (melanoma) xenograft model. Fulldetails of tumour studies are provided in the Examples ofPCT/US2011/053092 (WO2012/007896). Weekly administration of Ang2-h38c2or anti-IGF1R antibody (2.12.1.fx) inhibited Colo205 tumour growth.Combination of weekly administered Ang2-h38c2 and anti-IGF1R antibodyshowed an additive benefit on inhibiting Colo205 tumour growth. Weeklyadministration of MAC-2 alone showed similar benefit as the combination.In a separate study, MAC-2 dose-dependently inhibited Colo205 tumourgrowth and final tumour weights.

At day 28, tumour microvessel density after compound treated wassignificantly reduced (˜42%) by MAC-2 (10 mg/kg, once weekly) incomparison with the Vehicle-treated group confirming the anti-angiogenicactivity of the MAC-2 treatment.

To investigate whether MAC-2 targets both Ang2 and IGF1R in vivo, theeffects of MAC-2 on Ang2 and IGF1R expression levels were assessed in 2independent Colo205 xenograft tumors treated with Vehicle, Ang2-h38c2,IGF1R antibody (2.12.1.fx) or MAC-2 (dose response ranging from 0.3mg/kg to 10 mg/kg). The results showed that Ang2 and IGF1Rimmunoreactivity was significantly reduced by MAC-2 treatment in adose-dependent manner (1, 3 and 10 mg/kg) in comparison with theVehicle-treated group. The effect of MAC-2 on IGF1R levels was similarto that observed for an IGF1R antagonizing antibody. In addition, thelevels of phosphorylated IGF1R were reduced in tumours from MAC-2treated animals. These data demonstrate that MAC-2 treatment affectsboth Ang2 and IGF1R pathways in Colo205 xenograft model. MAC-2 treatmentdid not affect body weight gain and mice appeared to be in good healththroughout the studies. The anti-tumor efficacy of MAC-2 was alsoevaluated in an MDA-MB-435 melanoma xenograft model. Weeklyadministration of MAC-2 (3 and 20 mg/kg IP) resulted in a significant40% reduction (day 67) in tumor growth in the MDA-MB-435 model. Thus,MAC-2 demonstrates significant anti-tumor efficacy in 2 different humanxenograft tumor models.

Example 10 Peptide Conjugation Profile of Various Antibodies

The conjugation profiles of several different antibodies with peptideswere analyzed, using SEQ ID NO:27 and PEG₅ as an exemplary peptide andlinker respectively. All antibodies tested were human or fully humanizedIgG antibodies with well defined and characterized antigen interactions.hAbλTest comprises a CLλ (hIL22: SEQ ID NOs:136 and 137), whereas2.12.1.fx, mAbκTest1 (an IgG2 anti-Alk1 antibody, as disclosed inUS7537762, incorporated herein by reference), h38C2-IgG1 (SEQ ID NO:64and 65) and h38C2-IgG2 (SEQ ID NO:64 and 66) each comprise CLκ. Each ofthe antibodies were buffer exchanged into 20 mM HEPES, pH 7.0 andconcentrated to 5-20 mg/mL. [PFP-PEG₅-K¹¹-SEQ:27] was resuspended with50% propylene glycol and mixed with the relevant antibody at a 4.3:1molar ratio and allowed to react for at least 2 hrs at RT. All sampleswere diluted to 2 mg/ml and analyzed as an intact conjugated protein bysize exclusion chromatography-mass spectrometry (SEC-MS) to determinethe number and quantitation of conjugate forms of the protein. Thistechnique measures the molecular weight of each protein form; multiplepeptide conjugation sites are observed as distinct signals separated bythe mass difference of a bound peptide. Relative quantitation ofmultiple peptide conjugation species is performed by measuring thesignal magnitude. Table 22 shows the peptide conjugation profile ofvarious antibodies

For antibodies containing a CLκ, peptide conjugation occurs at adistribution between 0-4 peptide additions with the largest form being 2to 3 peptide additions. In contrast, for the CLλ comprising antibody,hAbλTest, conjugation of the peptide occurs at a distribution between0-4 peptides additions with the largest form being 1 to 2 peptideadditions.

The extent of peptide conjugation was examined separately on the lightand heavy chains. Each sample was denatured and disulfide bonds werereduced using guanidine hydrochloride and dithiothreitol. The resultingfree light and heavy chains were analyzed using LCMS to determine theconjugation profile on each. The peptide conjugation profile on thelight and heavy chain of various antibodies is shown in Table 27. On2.12.1.fx and hAbκTest1, the data demonstrate that the location ofconjugation is higher on the light chain; the most abundant form on thelight chain contains 1 peptide addition. Conjugation on the heavy chainis observed at a significantly lower level. On h38C2-IgG1 andh38C2-IgG2, comparable levels of conjugation are observed on the lightand heavy chain, with a slight conjugation preference on the lightchain. On a CLλ containing antibody (hAbλTest; comprising SEQ ID NOs:136and 137)), the majority of the conjugation occurs on the heavy chainwith a low level of conjugation observed on the light chain.

TABLE 27 Conjugation profile of various antibodies. CA (%) Avg LightChain % CA Heavy chain % CA Antibody 0 1 2 3 4 CA 0 1 2 0 1 2 2.12.1.fx1 15 53 26 5 2.2 20 70 9 84 16 0 hAbλTest 10 37 37 11 6 1.66 95 5 0 7422 4 hAbκTest1 7 10 35 27 14 2.55 11 74 14 87 13 0 h38C2 IgG1 1 3 28 5513 2.75 49 46 4 70 30 0 h38C2 IgG2 4 6 31 44 15 2.6 61 35 4 73 27 0Each of the antibodies 2.12.1.fx, hAbλTest and hAbKTest1 was assessedafter the conjugation process to determine the effect of the conjugationadditions on the ability of the antibody scaffold to retain its receptorbinding (compared to native mAb) (Table 28). The results show that thedirectional conjugation of peptides to the test antibodies did notappear to alter the antibody binding.

TABLE 28 Antibody binding to respective native antigen before and afterconjugation. Antigen binding Antibody Native (IC₅₀, nM) Afterconjugation (IC₅₀, nM) 2.12.1.fx 3.2 5.7 hAbλTest 0.4 1.7 hAbκTest1 5953

Example 11 Peptide Conjugation Profile of an IgG2-κ Antibody

The conjugation profile of an IgG2 κ antibody (hABKTest2) with a 39-merpeptide was analyzed (SEQ ID NO:164). The antibody was concentrated to 8mg/ mL and buffered exchanged into 40 mM HEPES pH 8.0. The peptide wasresuspended with 100% DMSO and mixed with the antibody at a 5.0:1 molarratio and allowed to react overnight at room temperature. All sampleswere diluted to 2 mg/ml and analyzed as an intact conjugated protein bysize exclusion chromatography-mass spectrometry (SEC-MS) to determinethe number and quantitation of conjugate forms of the protein. Thistechnique measures the molecular weight of each protein form; multiplepeptide conjugation sites are observed as distinct signals separated bythe mass difference of a peptide. Relative quantitation of multiplepeptide conjugation species is performed by measuring the signalmagnitude. Table 29 shows the peptide conjugation profile of hAbKTest2with the 39-mer peptide. The conjugation of peptide occurs at adistribution between 0-4 CA with an average of 2.03 CA, and isconsistent with directional conjugation on the CLκ-K⁸⁰.

TABLE 29 Conjugation profile of 39-mer peptide and hAbκTest2. Antibody %CA Avg scaffold Binding Peptide 0 1 2 3 4 CA hAbκTest2 39-mer peptide 122 53 18 5 2.03

In a separate experiment, the 39-mer peptide was conjugated toh38C2-IgG2 with MAL-PEG2-PFP as described above, at different molarconcentrations. In addition, binding of the cognate receptor for the39-mer peptide was assayed. The results (Table 30) shown are consistentwith directional conjugation at CLκ-K⁸⁰. Moreover, increasing theaverage number of peptides per antibody did not substantially increaseoverall binding to the target. This demonstrates that in certainscenarios, increasing the conjugation per antibody may not increasetarget binding, demonstrating one of the advantages of the invention;control of the number of peptides conjugating per antibody can helpachieve the maximum target binding per unit peptide.

TABLE 30 Conjugation profile of 39-mer peptide and H38C2-IgG2. 39-merpeptide:h38C2- CA (%) Avg # Peptide target: IgG2 mole ratio 0 1 2 3Conjugates EC50 (nM)   2:1 57 32 10 0 0.52 0.99 2.5:1 19 56 25 0 1.061.06   4:1 20 25 35 20 1.55 1.01   5:1 0 16 45 40 2.26 0.82

Example 12 Conjugation of Biotin to 2.12.1.fx Fab

The conjugation profile of the Fab region of 2.12.1.fx (SEQ ID NOs:4 and64) with PFP-Biotin was analyzed. The antibody Fab was concentrated to20 mg/ mL and buffered exchanged into 20 mM sodium acetate+ 200 mMtrehalose, pH 5.5 and spiked with 60 mM sodium phosphate pH 7.7.PFP-Biotin was resuspended with 100% DMSO and mixed with the antibody atsuccessive molar ratios and allowed to react overnight at roomtemperature. All samples were diluted to 2 mg/ml and analyzed as anintact conjugated protein by size exclusion chromatography-massspectrometry (SEC-MS) to determine the number and quantitation ofconjugate forms. This technique measures the molecular weight of eachprotein form; multiple conjugation sites are observed as distinctsignals separated by the mass difference of a conjugated peptide.Relative quantitation of multiple conjugation species is performed bymeasuring the signal magnitude. Table 31 shows the conjugation profileof 2.12.1.fx Fab with PFP-Biotin at molar ratios. The conjugation ofoccurs at a distribution between 0-2 additions as the molar ratioincreases. The lower number of molecules per antibody was consistentwith earlier results, based on the molar ratio used. This demonstratesthe flexibility of the process to control the amount of conjugation byaltering reaction parameters.

TABLE 31 Conjugation profile of Biotin to 2.12.1.fx Fab.

Binding Peptide:Antibody % CA Avg Peptide Molar Ratio  0  1  2 3 CABiotin-PFP 1:1 54 46 — — 0.46 Biotin-PFP 1.5:1   42 51  7 — 0.65Biotin-PFP 2:1 34 55 10 — 0.76 Biotin-PFP 3:1 28 55 17 — 0.88 Biotin-PFP4:1 21 46 26 8 1.21

Example 12 Conjugation of Biotin to h38C2-IgG1

The antibody h38C2-IgG1 was adjusted to 20 mg/mL with HEPES buffer pH7.5 to a final concentration of 0.02 M. Biotin-PFP was reconstituted inwater to 10 mg/mL and added to h38C2-IgG1 at a molar ratio of 5:1 andallowed to react at room temperature for 2 hrs. The unreacted PFP-Biotinwas removed by size exclusion chromatography and buffer exchanged into ahistidine, glycine, and sucrose buffer pH 6.5. The samples were dilutedto 2 mg/ml and analyzed as an intact conjugated protein by sizeexclusion chromatography-mass spectrometry (SEC-MS) to determine thenumber and quantitation of conjugate forms of the protein. Table 32shows the conjugation profile of h38C2-IgG1 with Biotin-PFP. Conjugationof h38C2-IgG1 occurs at a distribution between 0-3 CA with an average of1.1 conjugations. Increased conjugation would be possible followingoptimization of the reaction conditions. The reactivity of VH-K⁹⁹ (K⁹³according to Kabat numbering) on h38C2-IgG1 was confirmed to be >95%when reacted with the catalytic antibody test compound CATC-1, andanalyzed via reversed phase chromatography.

TABLE 32 Conjugation of Biotin and h38C2-IgG1.

Antibody  0  1  2  3 Avg CA h38C2-IgG1 16 61 20 3 1.1

Example 13 Conjugation Profile of 2.12.1.fx and CLκ-K⁸⁰, CLκ-K⁸² Mutants

Based on peptide mapping, there are 2 Lys in Y15 fragment. In order todistinguish the active conjugation site, CLκ-K⁸⁰ and CLκ-K⁸² weremutated to R respectively or in combination. Mutants of the testantibody, 2.12.1.fx, were generated following protocols described inQuickChange site-directed mutagenesis kit (Stratagene®). Mutations wereintroduced by oligonucleotide primers and confirmed by DNA sequencing.The mutated mAbs were transiently expressed in HEK 293 cells, andpurified using Protein A affinity column. The purified mAbs werecharacterized using MS. SEQ ID NOs:12, 13 and 14 show the mutant CLκsequences.

The antibody was buffer exchanged to 0.02M HEPES buffer pH 7.5 or 6.5 at2 mg/mL. If the pH was 6.5, the antibody was then spiked with 60 mMsodium phosphate pH 7.7. [PFP-PEG₅-K¹¹-SEQ:27] was resuspended with 50%propylene glycol and mixed with the protein at a 4.3:1 molar ratio andallowed to react overnight at RT. All samples were diluted to 2 mg/mland analyzed as an intact conjugated protein by size exclusionchromatography - mass spectrometry (SEC-MS) to determine the number andquantitation of conjugate forms of the protein. This technique measuresthe molecular weight of each protein form; multiple conjugation sitesare observed as distinct signals separated by the mass difference of aconjugated protein. Relative quantitation of multiple proteinconjugation species is performed by measuring the signal magnitude.Table 33 shows the conjugation profile of unmodified 2.12.1.fx,2.12.1.fx-[CLκ-K⁸⁰R] (CLκ: SEQ ID NO:12), 2.12.1.fx-[CLκ-K⁸²R] (CLκ: SEQID NO:13), and 2.12.1.fx-[CLκ-K⁸⁰R-K⁸²R] (CLκ: SEQ ID NO:14). CLκ-K⁸⁰Rmutant showed reduced conjugation. CLκ-K⁸²R had similar conjugation asthe unconjugated 2.12.1.fx. The conjugation of MAC-2 was lower thanobserved in other assays due using a combination HEPES/phosphate buffer.

TABLE 33 Conjugation profile of 2.12.1.fx, K⁸⁰ and R⁸² mutants. LC SEQID CA (%) NO: Mutants 0 1 2 3 4 Avg CA 6 MAC-2 14 49 31 5 1 1.29 12 K80R82 14 4 0 0 0.22 13 K82R 11 46 36 6 0 1.37 14 K80R/K82R 51 37 9 3 0 0.63

Example 14 Elucidation of Directional Conjugation Mechanism on K⁸⁰

CLκ-H⁸¹ side chain is very close to the ε-amino group of CLκ-K⁸⁰. SinceHis is often involved in proton transfer reactions, CLκ-H⁸¹ is verylikely required for CLκ-K⁸⁰ conjugation. In order to study the role ofCLκ-H⁸¹ in CLκ-K⁸⁰ site specific conjugation, the imidazole ring waseliminated by a CLκ-H⁸¹A mutation. CLκ-D⁴³A and CLκ-D⁴³A/H⁸¹A mutantswere made to study the role of CLκ-D⁴³ in site specific conjugation andthe combined effect of CLκ-D⁴³ and CLκ-H⁸¹.

Mutants were generated following protocols described in QuickChangesite-directed mutagenesis kit (Stratagene®). Mutations were introducedby oligonucleotide primers and confirmed by DNA sequencing. The mutatedmAbs were transiently expressed in HEK 293 cells, and purified usingprotein A affinity column. The purified mAbs were characterized usingMS. The following 2.12.1.fx I CLκ mutants were generated: CLκ-D⁴³A (SEQID NO:15), CLκ-K⁸⁰A (SEQ ID NO:16), CLκ-H⁸¹A (SEQ ID NO:17), CLκ-K⁸²A(SEQ ID NO:18) and CLκ-D⁴³A/H⁸¹A (SEQ ID NO:19).

Each of the antibodies was buffer exchanged to 20 mM sodium acetate, 200m trehalose pH 5.5 at 20 mg/ml. The proteins were then spiked with 60 mMsodium phosphate pH 7.7. [PFP-PEG₅-K¹¹-SEQ:27] was resuspended with 50%propylene glycol and mixed with the antibody at a 4.3:1 molar ratio andallowed to react overnight at room temperature. All samples were dilutedto 2 mg/ml and analyzed as an intact conjugated protein by sizeexclusion chromatography-mass spectrometry (SEC-MS) to determine thenumber and quantitation of conjugate forms of the protein. Thistechnique measures the molecular weight of each protein form; multipleconjugation sites are observed as distinct signals separated by the massdifference of a conjugated peptide. Relative quantitation of multipleconjugation species is performed by measuring the signal magnitude.

Table 34 shows the conjugation profile of 2.12.1.fx,2.12.1.fx-[CLκ-D⁴³A],

2.12.1.fx-[CLκ-K⁸⁰A], 2.12.1.fx-[CLκ-H⁸¹A], 2.12.1.fx-[CLκ-K⁸²A], and2.12.1.fx-[CLκ-D⁴³A/H⁸¹A] mutants. All the mutants showed reducedaverage conjugation level compared to the unmodified 2.12.1.fx antibody,except for CLκ-K⁸⁰A, which maintained directional conjugation.

The extent of conjugation was examined separately on the light and heavychains. Each sample was denatured and disulfide bonds were reduced usingguanidine hydrochloride and dithiothreitol. The resulting free light andheavy chains were analyzed using LCMS to determine the conjugationprofile on each. The conjugation profile on the light and heavy chain of2.12.1.fx and mutants are shown in Table 34. All the mutants listed inthe table showed reduced conjugation level on light chain compared tothe unmodified 2.12.1.fx except CLκ-K⁸⁰A. The heavy chain conjugationlevel of the mutants was at the similar level as the unmodified2.12.1.fx. The % of 1-LC % relative to the respective WT run is shown inthe right column, as described in Table 34.

TABLE 34 Conjugation profile of MAC-2 and K⁸⁰A, D⁴³ and H⁸¹ mutants. LCLC HC SEQ Avg Avg 1 LC ID CA (%) Avg LC CA% CA- HC CA % CA- WT NO:Mutants 0 1 2 3 4 CA 0 1 2 LC 0 1 2 HC % 6 MAC-2 1 15 53 26 5 2.2 23 698 0.85 86 14 0 0.14 15 D⁴³A 17 38 31 14 0 1.41 68 30 1 0.33 79 21 0 0.2143 16 K⁸⁰A 56 31 10 4 0 0.61 89 11 0 0.11 91 9 0 0.09 16 17 H⁸¹A 34 4417 6 0 0.95 89 11 0 0.11 78 22 0 0.22 16 18 K⁸²A 9 7 31 37 16 2.42 8 7715 1.06 83 17 0 0.17 111 19 D⁴³A/ 34 39 18 9 0 1.02 83 17 0 0.17 87 13 00.13 25 H⁸¹A

Example 15 Lambda/Kappa Substitution

The CLλ in hAbλTest1 (SEQ ID NOs:136 and 137) was substituted with CLκto determine whether this increased the level, directionality and/orcontrol of CL-specific conjugation. The CLλ/CLκ domain substitutionhybrid constructs were generated using overlap PCR. The VLλ and CLκ werePCR amplified using hAbλTest and a K mAb light chain as templatesseparately. These 2 PCR products were mixed as templates; hAbλTest1forward primer and LCLκ reverse primer were used in overlap PCR reactionto amplify the full length hAbλTestVL/CLκ DNA. The hybrid antibodyconstructs were transiently expressed in HEK 293 cells, and purifiedusing Protein A affinity column. The purified antibodies werecharacterized using MS. The hAbλTest CLκ hybrid bound to its cognateligand similarly to the native mAb (hAbλTest)(Table 35). SEQ ID NOs:59,60 and 61 are the light chain constant regions from hAbλTest,hAbλTest-λκ (with λJ), and hAbλTest-λκ J (with κJ).

TABLE 35 Antibody: Antigen binding of lambda/Kappa substitution.Inhibition of IL22 binding to hAbλTest1 Mutants LC SEQ ID NO: antigen(IC₅₀, nM) hAbλTest (CONTROL) 59 0.4 hAλTest-λκ 60 0.3 hAbλTest-λκJ 610.3

Example 16 hAbλTest1 Mutants: Motif Modification

To establish whether the short motif “KH” was sufficient for MACformation in the corresponding region of the CLλ, a mutant with simplesequence switch of residues CLλ^(81/82) in hAbλTest to place a histidinebeside K⁸⁰ was made, hence “K₈₀S⁸¹H₈₂” became “K⁸⁰H⁸¹S⁸²”. Mutants weregenerated following protocols described in QuickChange site-directedmutagenesis kit (Stratagene). Mutations were introduced byoligonucleotide primers and confirmed by DNA sequencing. The mutatedantibody constructs were transiently expressed in HEK 293 cells, andpurified using Protein A affinity column. The purified antibodies werecharacterized using MS. The hAbλTest-[CLλ-S⁸¹H/H⁸²S] (CL: SEQ ID NO:62)mutant bound to its ligand as well as the parent hAbλTest antibody did(Table 36).

TABLE 36 hAbλTest-S⁸¹H/H⁸²S. hAbλTest1 Mutants LC SEQ ID NO: Ligandbinding (IC₅₀, nM) hAbλTest (CONTROL) 59 0.3 hAbλTest-S⁸¹H/H⁸²S 62 0.4

Example 17 Conjugation Profile of hAbλTest1 Mutants

Each antibody (hAbλTest, hAbλTest-λκ, hAbλTest-λκJ andhAbλTest-[CLλ-S⁸¹H/H⁸²S]) was buffer exchanged to 20 mM sodium acetate,200 m trehalose pH 5.5 at 20 mg/ml. The proteins were then spiked with60 mM sodium phosphate pH 7.7. [PFP-PEG₅-K¹¹-SEQ:27] was resuspendedwith 50% propylene glycol and mixed with the antibody at a 4.3:1 molarratio and allowed to react overnight at room temperature. All sampleswere diluted to 2 mg/ml and analyzed as an intact conjugated protein bysize exclusion chromatography-mass spectrometry (SEC-MS) to determinethe number and quantitation of conjugate forms of the protein. Thistechnique measures the molecular weight of each protein form; multiplepeptide conjugation sites are observed as distinct signals separated bythe mass difference of a peptide. Relative quantitation of multiplepeptide conjugation species is performed by measuring the signalmagnitude. Table 37 shows the overall level of conjugation has beenincreased in the 2 LC-switched hybrids (λκ and λκJ—the former includes aλ J fragment, the latter includes a κ J fragment). The conjugation levelincreases over the hAbλTest control's average CA, going from 1.66 to2.19 (λκ) and 2.53 (λκJ) respectively. The mutant had little effectcompared to the native sequence, suggesting that “KH” motif alone is notsufficient for MAC formation.

The extent of peptide conjugation was examined separately on the lightand heavy chains (Table 37). Each sample was denatured and disulfidebonds were reduced using guanidine hydrochloride and dithiothreitol. Theresulting free light and heavy chains were analyzed using LCMS todetermine the conjugation profile on each. In the reduced analyses, theLC of native hAbλTest has only 5% 1CA but this jumps dramatically to 58%1 CA for hAbλTest-λκ and 63% 1 CA for hAbλTest-λκJ. The LC switch hadlittle effect on the level of HC conjugation, which remained fairlyconstant (except for λκJ, where HC conjugation increased moderately).Again, the mutant had little effect compared to the native sequence,suggesting that “KH” motif alone is not sufficient for MAC formation.The % of 1-LC % relative to the respective WT run is shown in the rightcolumn, as described in Table 37.

TABLE 37 Conjugation profile of hAbλTest mutants. LC SEQ Avg AvghAbλTest ID CA (%) Avg LC CA% CA- HC CA % CA- 1LC Mutants NO: 0 1 2 3 4CA 0 1 2 LC 0 1 2 HC WT % hAbλTest 59 10 37 37 11 6 1.66 95 5 0 0.05 7422 4 0.3 hAbλTest- 60 3 18 43 29 7 2.19 42 58 0 0.58 78 22 0 0.22 1160λκ hAbλTest- 61 2 11 34 36 17 2.53 33 63 4 0.71 64 36 0 0.36 1260 λκJhAbλTest- 62 7 34 37 16 6 1.79 82 18 0 0.18 79 21 0 0.21 360 S⁸¹H/H⁸²S

The receptor binding attributes of these conjugated forms was alsoassessed to determine the effect of conjugation with[PFP-PEG₅-K¹¹-SEQ:27] on the ability of the conjugated antibodies tostill bind to their ligand (Table 38).

TABLE 38 Antibody: Antigen binding of lambda at antibodies. SEQ ID NO:27 conjugated Inhibition of IL22 binding to hAbλTest1 Mutants LC SEQ IDNO: antigen (IC₅₀, nM) hAbλTest 59 1.7 hAbλTest-λκ 60 1.5 hAbλTest-λκJ61 1.6 hAbλTest1-S⁸¹H/H⁸²S 62 1.6

Example 18 MAC Generation Using Different Leaving Groups

To investigate if the degree of activation and/or structure of theactive ester leaving group was important in defining the directionalconjugation effect, a series of alternatively activated ester analogs of[PFP-PEG₂-MAL-K_(SH) ¹¹-SEQ:27] were synthesized. The distribution ofthe conjugate product was examined by MS of the intact conjugates, andthe degree of peptide addition to both the light and heavy chains werealso determined by MS following reduction of the intact conjugate andseparation of the light and heavy chains.

The structure and designations of the alternatively activated esters areshown below. The alternatively activated peptides were synthesized usingthe same strategies and methods shown above. Briefly, each activatedgroup was incorporated into a MAL-PEG₂-Z* linker, where Z* representedthe new leaving group replacing PFP. To synthesize the above compounds,a sample (30-40 mg) of the purified ABP-thiol peptide (i.e. ABP withK_(SH) as linking residue) was dissolved in anhydrous DMF (2 ml).MAL-PEG₂-Z* (20 mg) was added along with N-methylmorpholine (5 mL). Thereaction was stirred and monitored at RT by HPLC to follow thetime-course of product formation. The complete conversion of startingpeptide to activate-ester linked ABP product was observed within 2-6hrs. The solution was filtered and the product peak directly isolated bysemi-preparative HPLC. The products were isolated in yields ranging fromapproximately 30-50%, after lyophilization.

The conjugation reactions were carried out under the standardconditions. Briefly, the 2.12.1.fx antibody solution was prepared bydiluting the 2.12.1.fx solution with sodium phosphate, pH 7.7 to a finalconcentration of 0.06M. Separately, the peptide solution was prepared bydissolving the peptide to 20 mg/ml in propylene glycol, then dilutingthis solution to 10 mg/ml with water. For the conjugation reaction, thepeptide and antibody solutions were mixed at a 4:1 molar ratio for theprescribed period. For the time-course studies, samples of theconjugation solution were quenched at various time points by mixing asample of the conjugation reaction with a solution of 40 mM succinicacid, 200 mM glycine, pH 4.0 (1:1, v/v). Time-course of the conjugationreactions were followed by HPLC. SEQ ID NO:27 was used as an exemplarypeptide.

TABLE 39 Reactive esters- intact conjugation at 24 hrs.

Z8 Z9 Z2 Z3 Z4 Z5 Z6 Z7 NH5 2HI Z11 Z12 Z1 2,3,4 2,3,6 2,3,6 2,6 2,4 5,7NB2,3 1,3 Z10 2,6- 1 CA PFP TFP TFP TCP DCP DCN DCQ DCI D 4NP DFP NAP 0 3 32 17 100 81 38 73 34 20 41 50 100 1 34 45 43  0 19 45 25 40 36 42 39 0 2 51 20 30  0  0 16  2 18 31 15 11  0 3 12  3 11  0  0  2  0  5 12  3 0  0

Table 39 shows the final product distribution of the intact conjugates24 hrs after initiation of the conjugation reaction. The results showthat some of esters did not react at all (Z4, Z12), others reactedsluggishly (e.g. Z5), while several gave profiles approaching that ofPFP (Z1) (e.g. Z3).

Conjugation Kinetics

The rates of addition over time for each of the final conjugates areshown in Tables 39, 40, 41, and 42. 0CA represents underivatized2.12.1.fx antibody, whereas 1, 2 or 3CA represents additions of 1, 2 or3 peptides to the 2.12.1.fx antibody at each of the time periodsexamined.

TABLE 40 Conjugation kinetics of different Z* groups yielding 0 CA. 0CAZ8 Z9 Z2 Z3 Z4 Z5 Z6 Z7 NH5 2HI Z11 Z12 time Z1 2,3,4 2,3,6 2,3,6 2,62,4 5,7 NB2,3 1,3 Z10 2,6- 1 (hr) PFP TFP TFP TCP DCP DCN DCQ DCI D 4NPDFP nap 0 84 97 94 100 100 100 100 95 95 96 100 100 1 5 83 58 100 100 9596 43 24 79 93 100 2 4 75 40 100 100 89 93 42 20 67 88 100 4 4 62 27 10096 81 88 40 20 54 79 100 24 3 32 17 100 81 38 73 34 20 41 50 100

TABLE 41 Conjugation kinetics of different Z* groups yielding 1 CA. 1CAZ8 Z9 Z2 Z3 Z4 Z5 Z6 Z7 NH5 2HI Z11 Z12 time Z1 2,3,4 2,3,6 2,3,6 2,62,4 5,7 NB2,3 1,3 Z10 2,6- 1 (hr) PFP TFP TFP TCP DCP DCN DCQ DCI D 4NPDFP nap 0 16 3 6 0 0 0 0 5 5 5 0 0 1 38 17 36 0 0 5 4 39 39 21 8 0 2 3725 45 0 0 11 7 39 38 29 12 0 4 33 34 43 0 4 19 12 42 39 37 21 0 24 34 4543 0 19 45 25 40 36 42 39 0

TABLE 42 Conjugation kinetics of different Z* groups yielding 2 CA. 2CAZ8 Z9 Z2 Z3 Z4 Z5 Z6 Z7 NH5 2HI Z11 Z12 time Z1 2,3,4 2,3,6 2,3,6 2,62,4 5,7 NB2,3 1,3 Z10 2,6- 1 (hr) PFP TFP TFP TCP DCP DCN DCQ DCI D 4NPDFP nap 0 0 0 0 0 0 0 0 0 0 0 0 0 1 49 0 6 0 0 0 0 15 27 0 0 0 2 50 0 140 0 0 0 16 30 4 0 0 4 52 4 25 0 0 0 0 15 29 9 0 0 24 51 20 30 0 0 16 218 31 15 11 0

TABLE 43 Conjugation kinetics of different Z* groups yielding 3 CA. 3CAZ8 Z9 Z2 Z3 Z4 Z5 Z6 Z7 NH5 2HI Z11 Z12 time Z1 2,3,4 2,3,6 2,3,6 2,62,4 5,7 NB2,3 1,3 Z10 2,6- 1 (hr) PFP TFP TFP TCP DCP DCN DCQ DCI D 4NPDFP nap 0 0 0 0 0 0 0 0 0 0 0 0 0 1 8 0 0 0 0 0 0 3 11 0 0 0 2 10 0 2 00 0 0 3 12 0 0 0 4 12 0 5 0 0 0 0 4 12 0 0 0 24 12 3 11 0 0 2 0 5 12 3 00

Light and Heavy Chain Distribution

The extent of peptide conjugation for each of the alternativelyactivated esters was examined separately on the light and heavy chains.Each sample was denatured and disulfide bonds were reduced usingguanidine hydrochloride and dithiothreitol. The resulting free light andheavy chains were analyzed using LCMS to determine the conjugationprofile on each. The peptide conjugation profile on the light and heavychain of 2.12.1.fx and mutants are shown in Table 44. Almost all of theactivated peptides listed in the table showed reduced conjugation levelon light chain compared to the compound using PFP (Z1), except2,3,6-trifluorophenyl (Z3), which showed a similar level of conjugation.Activated esters derived from N-hydroxysuccinimide (NHS), i.e.N-Hydroxyl-5-norbornene-2,3-dicarboxylic acid imide and2-hydroxyl-isoindoline-1,3-dione (Z8 and Z9) showed a greater propensityfor heavy chain derivatization.

TABLE 44 Summary of activated ester results. Z* Z* Z* Time course ofconjugation adducts Reduced conjugation # Name Structure [separate 24 hrexpt in bold] at 24 hr 1 Penta- Fluoro- Phenyl

2 2,3,4- trifluoro- phenyl

3 2,3,6- trifluoro- phenyl

4 2,3,6- trichloro- phenyl

5 2,6- dichloro- phenyl

6 2,4 DiCl Napthalene

7 5,7- dichloro- quinolin- 8-yl

8 N- Hydroxyl- 5- norbornene- 2,3- dicarbox- ylic acid imide

9 2- hydroxyl- isoindoline- 1,3-dione

10 4-nitro- phenyl

11 2,6- difluoro- phenyl

12 1- naphthyl

Example 19

Further examples of alternatively activated esters are shown in Table45. The time-course of conjugation of several analogs of PFP esters wereexamined. By decreasing the number and position of the fluorine groupsin PFP, less reactive active ester forms can be synthesized andinvestigated. 2,3,5,6-tetrafluorophenyl ester and 2,4,6-trifluorophenylester were both tested after conjugation to [PEG₂-MAL-K_(SH) ¹¹-SEQ:27].1-hydroxyl-pyrrolidine-2,5-dione (NHS) was conjugated to[PEG₅-K¹¹-SEQ:27].

After 2 hrs conjugation, these less activated forms gave lower overallconjugation to 2.12.1.fx than PFP. NHS group also showed lower overallconjugation. NHS and PFP-containing peptides were conjugated to2.12.1.fx. The reduced forms were analyzed to see the distribution at 2hrs. PFP showed a much greater propensity for light chain derivatization(77% overall to LC, only 6% to heavy) compared to1-hydroxyl-pyrrolidine-2,5-dione (NHS) (31% overall to LC, but 34%overall to heavy).

TABLE 45 Alternatively activated esters- further examples. Activeesters- reduced analysis of Name Structure CA at 2 hr conjugation at 2hr  1 Penta- Fluoro- Phenyl

13 1- hydroxyl- pyrrolidine- 2,5- dione (NHS)

14 2,3,5,6- tetrafluoro- phenyl

15 2,4,6- trifluoro- phenyl

Compounds Z1-Z15 represent a variety of different structural types ofactive ester. It is enlightening to consider the series of fluorinatedaromatic active esters, which have a different number and pattern ofsubstitution of fluorine atoms around the aromatic ring (compounds Z1,Z2, Z3, Z11, Z14 and Z15) and consider how their structure influencestheir reactivity and propensity for protein derivatization. The kineticsof the antibody-conjugation of these derivatives can be convenientlycompared at the 2 hr time-point, when the pentafluorophenyl (Z1)reaction has gone to completion. With an increasing level of fluorinesubstitution around the ring, there is an increasing level of overallconjugation and a concomitant decrease in unreacted antibody. The rateof reaction is directly related to the pKa of the fluorinated phenolleaving group, with the most acidic phenols giving higher reactionrates. The rates of conjugation are Z1>Z14>Z3>Z15>Z2>Z11. The subtleeffects of the fluorine substitution patterns can be seen by comparingcompounds Z2, Z3 and Z15.

The structure of the active ester also significantly affected thedirectionality of the conjugation reaction. In general, the fluorinatedaromatic esters showed a marked propensity towards light chainderivatization (principally CLκ-K⁸⁰ as previously mentioned). Incontrast, several esters based on N-hydroxysuccinimide derivatives (Z8,Z9 and Z13) showed less preference, with often greater levels of heavychain derivatization observed.

Example 20

The rate of conjugation between MAC-1 (PEG₂-MAL-mercaptopropionyl linkerbetween the peptide and PFP activating group) and MAC-2(straight-chained PEG₅ linker between the peptide and PFP activatinggroup) was assessed. Table 46 compares these activated peptides to2.12.1×. The results show that the activated peptides behave verysimilarly in terms of the rate and extent of derviatization, despitetheir slightly different linker structures.

TABLE 46 Comparison of conjugation between MAC-1 and MAC-2. Intact timeMAC-2 MAC-1 (min) OCA 1CA 2CA 3CA 4CA OCA 1CA 2CA 3CA 4CA 0 72 27 1 0 082 18 1 0 0 10 26 56 17 1 0 29 49 20 2 0 20 13 53 29 5 0 15 47 33 5 0 309 51 32 8 1 9 43 40 8 0 40 7 45 39 9 1 8 41 41 8 2 50 6 43 39 11 1 7 4142 9 2 60 5 41 40 11 2 6 36 45 11 2 70 4 40 40 14 2 6 35 46 11 2 80 3 3844 14 2 5 36 47 10 2 90 4 37 45 13 1 6 35 46 12 2 100 4 40 41 13 2 6 3546 11 2 110 3 40 42 14 1 6 34 46 12 3 120 4 37 44 13 1 5 35 46 12 2

Example 21 Effect of Linker Length

The effect on the final conjugate distribution profile of havingdifferent lengths of linker was examined. Compounds were synthesizedwith different PEG length linkers joining the peptide to the PFP group.The results for the addition to 2.12.1.fx of 0, 1, 2, 3 and 4 peptidesare summarized in Table 47. Overall, changing the length of the PEGlinker had generally little effect on the distribution of conjugatesobtained.

TABLE 47 Effect of linker length.

  CA (%) n  0  1  2  3 4  2  8 39 44  8 0  3  6 34 47 10 2  5  4 37 4413 1  7  4 35 49 11 0  9  3 28 49 19 2 13  3 32 54 10 0 17  6 37 51  7 021  4 43 45  5 2 25 11 44 38  7 0

Structure of Example 21 compounds.

2.12.1.fx was conjugated to [PFP-PEG_(n)-K¹¹-SEQ:27]

Example 22 Conjugation of Alternative Peptide Sequences

To confirm the applicability of the invention across other peptidesequences, SEQ ID NO:80 and SEQ ID NO:81 (Test-peptides-1, and -2) wereconjugated. SEQ ID NOs:80 and 81 were conjugated with [PFP-PEG₅] andthen the 2.12.1.fx under conditions previously optimized for reactionwith [PFP-PEG₅-K¹¹-SEQ:27]. The results of analysis of the conjugationprofile and LC/HC conjugation are shown in Table 48. SEQ ID NO:80 andSEQ ID NO:81 both showed directional conjugation to the light chain. Onfurther analysis of the LC/HC distributions, similar profiles to that ofMAC-2 were observed, with around 70% LC derivatization and less than 10%on the HC.

TABLE 48 Conjugation profile of SEQ ID NO 80 and SEQ ID NO: 81. LC % CAHC % CA SEQ % CA LC + LC + HC + HC + ID NO:  0  1  2  3 4 LC 1 2 HC 1 227  2 24 55 17 3 24 65 11 91 9 — 80 11 39 43  8 0 32 68 — 95 5 — 81  835 48 10 0 29 71 — 94 6 —

 

Example 23 Summary of Peptide Conjugation Analysis

Peptide mapping experiments were performed on a range ofprotein/conjugate combinations for the purpose of confirming theimportant parameters that lead to directional conjugation at CLκ-K⁸⁰ onantibody light chains. Table 49 lists the results of the peptide mappingexperiments performed. For each study parameter, the peptide mappingprocedure described earlier was used. “***” indicates a high level ofdirectional conjugation to CLκ-K⁸⁰. “**” and to a lesser extent, “*”,indicates directional conjugation is still observed, but may showdifferences, such as slower reaction conditions, less overallconjugation, or averaging at one light chain only, and so may be moresuitable to special circumstances, such as generating MACs with between0.5 and 1.5 peptide per antibody (for example). “−” indicates that thesereaction conditions did not appear favorable towards directionalconjugation at CLκ-K⁸⁰.

As CLκ-K⁸⁰ was observed in MAC-2 to be the location of directionalconjugation, peptide mapping studies on alternative parameters focusedon this location. Detailed peptide mapping data for each study parameteris not included, but significant conjugation levels at other K residueswas not observed, and observations of other MACs were consistent withdirectional conjugation at CLκ-K⁸⁰.

CLκ-K⁸⁰R and CLκ-K⁸⁰A mutations of 2.12.1.fx resulted in the loss ofdirectional conjugation at this site; suggesting an essential role forthis specific residue. CLκ-K⁸²R, and CLκ-K⁸²A mutations did not hinderdirectional conjugation to CLκ-K⁸⁰, and may even enhance it. Of theother study parameters examined, at least a portion of the sub-type oflight chain constant region was observed to have a significant impact ondirectional conjugation; at least a portion of the light chain sub-typekappa was determined to be necessary. Conjugation onto a CLλ sub-type(using an exemplary λ containing antibody, hAbλTest1), did notdemonstrate directional conjugation. When the CLλ of hAbλTest1 wasmutated to a CLκ, directional conjugation at K⁸⁰ was recovered.

TABLE 49 Summary of directional conjugation at CLκ-K⁸⁰. Mutations/Differences SEQ Directional Antibody LC Vs MAC1/2 ID NO Linker Z*conjugation 2.12.1.fx κ 27 PEG₂-MAL PFP * * * 2.12.1.fx κ 27 PEG₅PFP * * * 2.12.1.fx Fab κ 27 PEG₅ PFP * * * h38C2-IgG1 κ 27 PEG₅PFP * * * h38C2-IgG2 κ 27 PEG₅ PFP * * * hAbλTest λ K⁸⁰SH 27 PEG₅ PFP —hAbκTest1 κ 27 PEG₅ PFP * * * hAbκTest3 κ 39-mer PEG₅ PFP * * * hAbλTestλκ 27 PEG₅ PFP * * * hAbλTest λκJ 27 PEG₅ PFP * * * 2.12.1.fx κ K⁸⁰R 27PEG₅ PFP — 2.12.1.fx κ K⁸²R 27 PEG₅ PFP * * * 2.12.1.fx κ K⁸⁰R/R⁸²R 27PEG₅ PFP — 2.12.1.fx κ D⁴³A 27 PEG₅ PFP * * 2.12.1.fx κ K⁸⁰A 27 PEG₅ PFP— 2.12.1.fx κ H⁸¹A 27 PEG₅ PFP — 2.12.1.fx κ K⁸²A 27 PEG₅ PFP * * *2.12.1.fx κ D⁴³A/H⁸¹A 27 PEG₅ PFP — hAbλTest1 λ S⁸¹H/H⁸²S 27 PEG₅ PFP —2.12.1.fx κ 39-mer PEG₅ PFP * * * 2.12.1.fx κ 80 PEG₅ PFP * * *2.12.1.fx κ 81 PEG₅ PFP * * * h38C2-IgG2 κ 39-mer PEG₅ PFP * * *2.12.1.fx Fab κ biotin PEG₅ PFP * * * 2.12.1.fx κ 27 PEG₂-MAL PFP * * *2.12.1.fx κ 27 PEG₂-MAL 2,3,4 TFP (2) * * 2.12.1.fx κ 27 PEG₂-MAL 2,3,6TFP (3) * * 2.12.1.fx κ 27 PEG₂-MAL 2,3,6 TCP (4) — 2.12.1.fx κ 27PEG₂-MAL 2,6 DCP (5) — 2.12.1.fx κ 27 PEG₂-MAL 2,4 DCN (6) * 2.12.1.fx κ27 PEG₂-MAL 5,7 DCQ (7) — 2.12.1.fx κ 27 PEG₂-MAL NH-5-N2,3DI (8) *2.12.1.fx κ 27 PEG₂-MAL 2Hi1,3 DIO (9) * 2.12.1.fx κ 27 PEG₂-MAL 4NP(10) * * 2.12.1.fx κ 27 PEG₂-MAL 2,6 DFP (11) * * 2.12.1.fx κ 27PEG₂-MAL NAP (12) — 2.12.1.fx κ 27 PEG₂-MAL 1HP 2,5D (13) * 2.12.1.fx κ27 PEG₂-MAL 2,3,5,6 TFP (14) * * 2.12.1.fx κ 27 PEG₂-MAL 2,4,6 TFP(15) * * 2.12.1.fx κ 27 PEG₂-MAL Squarate * 2.12.1.fx κ 27 PEG₂-MALAZD * 2.12.1.fx κ 27 PEG₂₋₁₇ PFP * * * 2.12.1.fx κ 27 PEG₁₇₋₂₁ PFP * *2.12.1.fx κ 27 PEG₂₅ PFP * *

Example 24 Examination of CLκ-D⁷⁷

Residues geographically close to the CLκ-K⁸⁰ in the 3-D structure wereexamined. Initial Crystal structure analysis suggested the possibilitythat CLκ-D⁷⁷ could form a salt bridge with CLκ-K⁸⁰, which could have animpact on the CLκ-K⁸⁰ directional conjugation. In order to study theeffect of CLκ-D⁷⁷ on conjugation to CLκ-K⁸⁰, CLκ-D⁷⁷ was mutated toCLκ-A⁷⁷ on the 2.12.1.fx antibody to create 2.12.1.fx-[CLκ-D⁷⁷A] (CLκ ofSEQ ID NO:37). The CLκ-D⁷⁷A mutation was generated on an antibody lightchain following protocols described in QuickChange site-directedmutagenesis kit (Stratagene®). The mutation was introduced byoligonucleotide primers and confirmed by DNA sequencing.2.12.1.fx-[CLκ-D⁷⁷A] was transiently expressed in HEK 293 cells, andpurified using Protein A affinity column. The purified mAbs werecharacterized using MS.

2.12.1.fx and 2.12.1.fx-[CLκ-D⁷⁷A] (1 mg reaction size) were adjusted to18 mg/ml to pH 7.7 with a phosphate buffer to a final concentration of0.06M sodium phosphate. The exemplary test peptide-linker pair[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 10 mg/ml. [PFP-PEG₅-K¹¹-SEQ:27] was added to antibody at a molarratio of 4.3:1 and allowed to react for 2 hrs at RT. The conjugatedproduct was diluted to 2 mg/ml and analyzed as an intact conjugatedprotein by SEC-MS to determine the number and quantitation of conjugateforms of the protein. Relative quantitation of multiple peptide-linkerconjugation species was performed by measuring the signal magnitude.

Table 50 compares the conjugation profile of[2.12.1.fx]-[PEG₅-K¹¹-SEQ:27] and[2.12.1.fx-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ:27]. The conjugation profile of[2.12.1.fx]-[PEG₅-K¹¹-SEQ:27] occurs as a distribution between 0-4peptide additions with the largest form being 2 peptide additions andthe average number of peptide additions is 2.16. The profile changeswhen the residue CLκ-D⁷⁷ is mutated to CLκ-A⁷⁷ in the scaffold protein;the average number of peptide additions rises to 2.38 and significantlyless single peptide addition is observed. This result suggests that thesingle point mutation CLκ-D⁷⁷A has the effect of increasing the overallconjugation to the scaffold. In both conditions replicate analysis (n=3)demonstrates that the conjugations profiles observed are reproducible.

The extent of peptide conjugation was examined separately on the lightand heavy chains of 2.12.1.fx and 2.12.1.fx-[CLκ-D⁷⁷A]. The producedMACs were denatured and disulfide bonds were reduced using guanidinehydrochloride and dithiothreitol. The resulting free light and heavychains were analyzed using LCMS to determine the conjugation profile oneach. Table 50 demonstrates that the average conjugation is higher onthe light chain of 2.12.1.fx-[CLκ-D⁷⁷A] than 2.12.1.fx; the averageconjugate addition value for 2.12.1.fx-[CLκ-D⁷⁷A] is 1.15 compared to0.85 for 2.12.1.fx. In addition, unconjugated light chain is undetectedin 2.12.1.fx-[CLκ-D⁷⁷A]. Conjugation on the heavy chain is observed at asignificantly lower level. The majority of observed heavy chain for both2.12.1.fx and 2.12.1.fx-[CLκ-D⁷⁷A] is unconjugated; this is especiallytrue in the case of 2.12.1.fx-[CLκ-D⁷⁷A] heavy chain. These resultssuggest that the CLκ-D⁷⁷A mutation alters the light chain to make itsignificantly more susceptible to conjugation. Replicate analysis ofthis experiment by multiple scientists is shown in Table 50 whichdemonstrates that the profile of conjugation is consistent andreproducible.

TABLE 50 Analysis of conjugation of [PEG₅-K¹¹-SEQ: 27] to Abs 2.12.1.fx(WT) and 2.12.1.fx-[CLκ-D⁷⁷A]. Rep = replicate. AvReps is the average ofthe results of the three replicate experiments, with the standarddeviation shown beneath (StdDev). Ab % CA shows % conjugations additionsper antibody, followed by the average CA per antibody. Ab % CA Avg. LC %CA Avg. HC % CA Avg. Ab 0 1 2 3 4 CA 0 1 2 CA 0 1 CA WT Rep1 1 17 56 224 2.11 21 72 7 0.86 86 14 0.14 Rep2 2 14 54 25 5 2.18 25 67 8 0.83 85 150.15 Rep3 2 13 55 25 6 2.2 23 69 8 0.85 85 15 0.15 Av. Rep 2 15 55 24 52.16 23 69 8 0.85 85 15 0.15 StdDev 1 2 1 2 1 0.05 2 3 1 0.02 1 1 0.01D⁷⁷A Rep1 5 4 54 30 8 2.32 0 84 16 1.16 94 6 0.06 Rep2 6 4 43 36 12 2.440 85 15 1.15 94 6 0.06 Rep3 3 3 56 31 7 2.37 0 86 14 1.14 94 6 0.06AvRep 5 4 51 32 9 2.38 0 85 15 1.15 94 6 0.06 StdDev 2 1 7 3 3 0.06 0 11 0.01 0 0 0.00Reduced light and heavy chain analysis also shown, with respectiveaverage CA per chain. CLκ-D⁷⁷A shows 123% rate of LC % 1CA speciescompared to native CLκ.

Example 25 Peptide Mapping Characterization of2.12.1.fx-[CLκ-D⁷⁷A]-[SEQ:27-K¹¹-PEG5] Heavy and Light Chain ReferenceProduct

2.12.1.fx-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ:27] conjugated antibody was reducedwith dithiothreitol and cysteine residues were alkylated bycarboxymethylation with iodoacetamide. Chymotrypsin was used forproteolytic digestion. Digested fragments in solution were analyzedusing LCMS. Individual fragments were separated over a 018 HPLC columnand their accurate mass was measured in a Q-T of mass spectrometer. Theresulting fragment mass was used to identify unmodified fragments orfragments modified with a [PEG₅-K¹¹-SEQ:27] conjugation group. Thisexperiment was interpreted by focusing on chymotryptic fragments thatcontain a lysine residue and are therefore possible sites for peptideconjugation. Tables 51 and 52 list of all such fragments on the heavychain and light chains respectively. Blank entries are fragments thatwere not detected using this technique. Detected fragments that wereobserved with a [PEG₅-K¹¹-SEQ:27] modifier are considered potentialsites of peptide conjugation.

2 [PEG₅-K¹¹-SEQ:27]-conjugated fragments were detected using LCMSpeptide mapping of the 2.12.1.fx-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ:27] product.Both of these conjugated fragments were present on the light chain ofthe 2.12.1.fx-[CLκ-D⁷⁷A] antibody. In comparison, 8 fragments conjugatedto [PEG₅-K¹¹-SEQ:27] were detected in 2.12.1.fx -[PEG₅-K¹¹-SEQ:27].

Overall, these results suggest that conjugation levels in the CLκ-D⁷⁷Amutant are elevated at fewer conjugation sites, possibly suggestingincreased conjugation specificity relative to the unmutated antibody.Further, structural analysis has shown that the CLκ-D⁷⁷ residue is inclose proximity (<10 Ås) to the identified major conjugation siteCLκ-K⁸⁰. It was speculated that an electrostatic interaction, possibly asalt bridge, could exist between the carboxylic acid of CLκ-D⁷⁷ and theprimary amine of CLκ-K⁸⁰. The CLκ-D⁷⁷A mutation would disrupt such anelectrostatic interaction, resulting in the reactive amine on CLκ-K⁸⁰being more exposed and susceptible to conjugation with the reactiveesters of the invention. Although subsequent analysis coupled withsophisticated modeling helped build a more complete picture of thereaction site, and indicated that CLκ-D⁷⁷ exerted its effect primarilythrough its interaction with CLκ-H81, the initial hypothesis of aninteraction between CLκ-D⁷⁷ and CLκ-K⁸⁰ was helpful in underlining thesignificance of the CLκ-D⁷⁷ residue.

The observed conjugation sites in the2.12.1.fx-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ:27] product are light chainchymotrypsin fragments Y3 and Y15. Analysis of the signal intensitiesfor these fragments suggests that fragment Y15, which carries theCLκ-K⁸⁰ residue, is the primary conjugation site. Fragment Y15 is onlyobserved as an [PEG₅-K¹¹-SEQ:27]-modified fragment at a very high signalintensity (1118572 counts, Table 52), whilst the unmodified form of Y15is not observed, suggesting that all or nearly all of fragment Y15exists in the modified form. Fragment Y3 is observed in both the[PEG₅-K¹¹-SEQ:27]-modified and unmodified forms; unmodified Y3 signalintensities in 2.12.1.fx-[PEG₅-K¹¹-SEQ:27] and2.12.1.fx-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ:27] are within 15%.[PEG₅-K¹¹-SEQ:27]-modified Y3 is observed at a relatively low level(9737 counts, Table 52).

The table entries for Tables 51 and 52 are explained below:Fragment number: Chymotrypsin fragments numbering from the N-terminus;joined fragments (ie—Y1-2) indicate a missed cleavage site.Start/End: Numbering of the fragment location from the N-terminus.Fragment Mass (Da): Theoretical mass of the fragment listed in Daltons.Retention Time (Control/Analyte): Time of chromatographicretention/elution in the LCMS peptide mapping experiment.MS Signal Intensity (Control/Analyte): Magnitude of observed signalobserved by MS.Mass Error—ppm (Control/Analyte): Comparison of theoretical vs. observedmass of the peptide fragment; values closer to zero (0) demonstratebetter mass accuracy. The control protein for Retention Time, MS signalintensity and Mass Error is 2.12.1.fx-[CLκ-D⁷⁷A] and the analyte proteinin each case is 2.12.1.fx-[CLκ-D⁷⁷A]+[PEG₅-K¹¹-SEQ:27].Modifiers: Potential covalent additions to the fragment;[PEG₅-K¹¹-SEQ:27]- antibody binding peptide of Lysine residue, CAM-carboxymethylation of Cysteine residue.

TABLE 51 Peptide mapping characterization of 2.12.1.fx-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ: 27] heavy chain reference product. Fragment FragmentRetention Time MS Signal Intensity Mass Error (ppm) Number Start EndMass (Da) Control Analyte Control Analyte Control Analyte Modifiers Y1 127 2617.3533 Y1-2 1 29 2865.4695 Y5-6 34 47 1657.8398 Y6 37 47 1253.68819.2 19.2 516640 548267 1.9 0 Y6-7 37 50 1602.8518 22.1 22.1 26537 31229−1.6 −2 Y8-9 51 68 1931.9337 16.5 16.5 60894 82459 −2.2 0.5 Y9 61 68878.461 11.3 11.4 376224 403402 0 −0.3 Y9-10 61 80 2241.1501 Y10 69 801380.6997 13.3 13.3 261813 286406 −1.1 0.3 Y10-011 69 94 2972.4661Y19-20 111 157 4748.2773 Y20 116 157 4160.0405 Y20-21 116 166 5202.5527Y20-21* 116 166 5316.5957 34.1 34.1 6445 8275 0.5 −5.7 CAM(2) Y24-25 202245 4702.2109 Y25 207 245 4151.9722 Y25* 207 245 4437.0796 20.9 20.91495322 1771622 1.1 0.7 CAM(5) Y25-26 207 279 7985.9092 Y26 246 2793851.9478 Y26-27 246 281 4152.0698 Y28-29 282 300 2245.1128 Y29 283 3002082.0493 14.6 14.6 20665 18618 −0.6 −0.2 Y29-30 283 304 2531.2405Y31-32 305 323 2241.1907 Y32 318 323 722.3599 7.9 7.9 93966 81618 0.1 3Y32 318 323 722.3599 17.7 18.4 37943 11371 11.4 27.1 Y32 318 323722.3599 18.4 11761 23.8 Y32-33 318 353 4028.188 Y33 324 353 3323.838620 5422 3.1 Y33* 324 353 3380.8601 19.7 19.7 2196329 2374835 −2.5 −3.8CAM(1) Y33-34 324 376 5883.1577 Y34 354 376 2577.3293 Y34-35 354 3853637.8159 Y34-35* 354 385 3694.8374 33 33 10095 10026 1.9 −2 CAM(1)Y36-37 386 408 2527.0808 Y37 396 408 1394.6388 19.6 19.6 62942 65871−0.9 −1.6 Y37-38 396 409 1541.7072 25.1 25.1 827336 874876 0 −3.8 Y39-40410 421 1494.8195 Y40 412 421 1218.672 15.8 15.8 77917 78774 −0.3 0.2Y40-41 412 427 1891.9905 20.3 20.3 107513 150305 0.2 0.1 Y42-43 428 4502525.1792 Y43 441 450 1016.5502

TABLE 52 Peptide mapping characterization of2.12.1.fx-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ: 27] light chain reference product.Fragment Peptide Mass Retention Time MS Signal Intensity Mass Error(ppm) Number Start End (Da) Control Analyte Control Analyte ControlAnalyte Modifiers Y2-3 36 49 1688.9725 16.2 16.2 145374 172582 −1.7 −1.1Y3 37 49 1525.9093 15.5 15.5 331068 390175 −2.7 −2.4 Y3* 37 49 3218.759324 9737 −6.8 [SEQ: 27-K11- PEG5](1) Y3-4 37 62 2882.6355 Y9-10 88 1163244.729 Y10 99 116 1871.0992 Y10-11 99 139 4331.335 Y11 117 1392478.2463 22.8 61217 −1.7 Y11* 117 139 2535.2678 21.5 5127 −16.8 CAM(1)Y11-12 117 148 3635.8445 Y12 140 148 1175.6088 Y12-13 140 173 3886.8245Y13 149 173 2729.2263 13.1 13.1 1140556 1153543 −1.1 −1.8 Y13-14 149 1864051.9346 Y14 174 186 1340.7188 Y14-15 174 192 2125.1418 Y15 187 192802.4337 7.5 275639 −1.9 Y15* 187 192 2495.2837 20.9 1118572 −6.3 [SEQ:27-K11- PEG5](1) Y15-16 187 209 2574.29 Y16 193 209 1789.8668 18.7 54004.4 Y16* 193 209 1846.8883 18.1 18.1 169490 246823 −1.7 −2.2 CAM(1)Y16-17 193 214 2349.0842 17.8 9211 0.1

Example 26 Examination of CLκ-D⁷⁷ Mutations

CLκ-D⁷⁷ residue of 2.12.1.fx antibody was mutated to each of the other18 amino acids in addition to the CLκ-D⁷⁷A mutation. The CLκ-D⁷⁷G (SEQID NO:38), CLκ-D⁷⁷L (SEQ ID NO:40), CLκ-D⁷⁷S (SEQ ID NO:49), CLκ-D⁷⁷E(SEQ ID NO:53), and CLκ-D⁷⁷R (SEQ ID NO:54) and mutants were generatedfollowing protocols described in QuickChange site-directed mutagenesiskit (Stratagene®). Mutations were introduced by oligonucleotide primersand confirmed by DNA sequencing. The other 13 mutants on the CLκ-D⁷⁷site (CLκ-D⁷⁷V (SEQ ID NO:39), CLκ-D⁷⁷I (SEQ ID NO:41), CLκ-D⁷⁷P (SEQ IDNO:42), CLκ-D⁷⁷F (SEQ ID NO:43), CLκ-D⁷⁷W (SEQ ID NO:44), CLκ-D⁷⁷Y (SEQID NO:45), CLκ-D⁷⁷H (SEQ ID NO:46), CLκ-D⁷⁷M (SEQ ID NO:47), CLκ-D⁷⁷C(SEQ ID NO:48), CLκ-D⁷⁷T (SEQ ID NO:50), CLκ-D⁷⁷Q (SEQ ID NO:51),CLκ-D⁷⁷N (SEQ ID NO:52), CLκ-D⁷⁷K (SEQ ID NO:55)) were generatedfollowing protocols described in Quick PCR Cloning Kit (BPS Bioscience).Mutations were introduced by oligonucleotide primers and cloned to amodified p2.12.1.fxP4 vector (Invitrogen) cut with BglII and NheI.Insert DNA were confirmed by DNA sequencing. The mutated mAbs weretransiently expressed in HEK 293 cells, and purified using protein Aaffinity column. The purified mAbs were characterized using MS.

2.12.1.fx and 2.12.1.fx mutants were adjusted 18 mg/ml to pH 7.7 with aphosphate buffer to a final concentration of 0.06 M sodium phosphate.[PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in a propylene glycol solutionto 10 mg/ml. The peptide/linker was added to antibody at a molar ratioof 4.3:1 and allowed to react for 2 hrs at RT.

Table 53 describes the overall conjugation profile of the CLκ-D⁷⁷mutants. CLκ-D⁷⁷C aggregated due to an introduction of a free cysteine,and the results were not interpretable. Mutations CLκ-D⁷⁷W, CLκ-D⁷⁷M,CLκ-D⁷⁷H, CLκ-D⁷⁷Q, CLκ-D⁷⁷N, and CLκ-D⁷⁷V did not change the overallconjugation profile compared to wild-type 2.12.1.fx.

Mutations CLκ-D⁷⁷F, CLκ- CLκ-D⁷⁷K, CLκ-D⁷⁷Y, and CLκ-D⁷⁷E decreased theoverall level of conjugation. Mutations CLκ-D⁷⁷P, CLκ-D⁷⁷I, CLκ-D⁷⁷T,CLκ-D⁷⁷R, CLκ-D⁷⁷L, CLκ-D⁷⁷S, and CLκ-D⁷⁷G increased the level ofconjugation.

Analysis of the reduced LC and HC showed that only the mutationsCLκ-D⁷⁷F, CLκ- D⁷⁷K, CLκ-D⁷⁷Y, CLκ-D⁷⁷E, and CLκ-D⁷⁷C resulted inreduced levels of conjugation on the light chain. The levels ofconjugation on the light chain increased (and conjugation on the heavyslightly decreased) for CLκ-D⁷⁷M, CLκ-D⁷⁷H, CLκ-D⁷⁷Q, CLκ-D⁷⁷N, CLκ-D⁷⁷Wand CLκ-D⁷⁷V. Mutations CLκ-D⁷⁷P, CLκ-D⁷⁷I, CLκ-D⁷⁷T, CLκ-D⁷⁷R,CLκ-D⁷⁷L, CLκ-D⁷⁷S, and CLκ-D⁷⁷G increased the level of conjugation onthe light chain by reducing the level of unconjugated light chain.CLκ-D⁷⁷K increased the level of 2 conjugates on the light chain due tothe introduction of another lysine, a potential conjugation site.

TABLE 53 Conjugation analysis of CLκ-D⁷⁷ mutants to alternative aminoacids (data is separated within the table according to the proteinamount used during the conjugation reaction, or because the conjugationreaction was set up at a different time). Ab % CA Avg. LC % CA Avg. HC %CA Avg. 1LC Ab 0 1 2 3 4 CA 0 1 2 CA 0 1 CA WT % WT 1 16 54 24 4 2.14 1969 13 0.94 88 12 0.12 D⁷⁷R 6 12 41 26 15 2.33 8 87 5 0.96 94 6 0.06 126D⁷⁷L 5 5 53 28 10 2.33 1 88 11 1.11 91 9 0.09 127 D⁷⁷E 8 27 39 18 8 1.9032 57 10 0.78 84 16 0.78 82 D⁷⁷S 5 6 47 29 12 2.36 0 92 8 1.08 94 6 0.06133 D⁷⁷G 7 7 44 28 13 2.34 0 91 9 1.09 92 8 0.08 131 WT 2 24 50 21 31.99 24 66 10 0.85 90 10 0.1 D⁷⁷Q 2 10 78 10 1.96 15 81 4 0.88 96 4 0.04122 D⁷⁷P 3 4 63 24 7 2.26 5 88 7 1.02 96 4 0.04 133 D⁷⁷K 9 30 36 17 81.84 34 45 21 0.86 93 7 0.07 68 D⁷⁷N 3 8 79 11 1.98 11 83 6 0.94 96 40.04 125 D⁷⁷Y 28 41 19 11 1.14 54 42 4 0.51 89 11 0.11 63 D⁷⁷V 6 10 6321 1.98 13 79 9 0.96 95 5 0.05 119 D⁷⁷I 3 4 63 24 7 2.27 6 85 9 1.03 937 0.07 128 D⁷⁷T 3 11 59 18 9 2.17 8 88 4 0.97 95 5 0.05 133 WT 4 30 4420 3 1.88 28 63 10 0.82 89 11 0.11 D⁷⁷M 4 15 67 14 1.90 16 81 3 0.87 964 0.04 132 D⁷⁷F 21 42 24 13 1.29 54 42 4 0.49 86 14 0.14 66 D⁷⁷H 5 16 6019 1.92 16 75 9 0.93 94 6 0.06 119 WT 5 36 47 12 1.66 30 60 10 0.8 90 100.1 D⁷⁷W 8 29 46 18 1.73 20 75 4 0.84 91 9 0.09 125 D⁷⁷C 60 37 2 0.42 955 0.05 61The decreased level of conjugation for the tests run at 0.5 and 0.25mg/ml was due to the low levels of the antibody. Ab % CA shows %conjugations additions per antibody, followed by the average CA perantibody. Reduced light and heavy chain analysis also shown, withrespective average CA per chain. The % of 1-LC % relative to therespective WT run is shown in the right column: for example, D⁷⁷Q; 1-LC% value of 81 is 126% of the respective WT 1-LC % of 69 for thatexperimental run. All samples were tested with 1 mg Ab, except the runincluding D⁷⁷M, D⁷⁷F and D⁷⁷H (0.5 mg), and the run including D⁷⁷W andD⁷⁷C (0.25 mg).

Example 27 Effects of Other Mutations to the CHκ Region on Conjugation

In addition to CLκ-D⁷⁷A, other residues within 10A distance to CLκ-K⁸⁰were mutated to alanine: CLκ-K⁴¹A (SEQ ID NO:20), V⁴²A (SEQ ID NO:21),CLκ-D⁴³A (SEQ ID NO:56), CLκ-N⁴⁴A (SEQ ID NO:22), CLκ-L⁴⁶A (SEQ IDNO:23), CLκ-Q⁴⁷A (SEQ ID NO:24), CLκ-S⁴⁸A (SEQ ID NO:25), CLκ-N⁵⁰A (SEQID NO:26), CLκ-L⁷³A (SEQ ID NO:28), CLκ-S⁷⁴A (SEQ ID NO:29), CLκ-K⁷⁵A(SEQ ID NO:30), CLκ-Y⁷⁸A (SEQ ID NO:31), CLκ-E⁷⁹A (SEQ ID NO:32),CLκ-H⁸¹A (SEQ ID NO:33), CLκ-V⁸³A (SEQ ID NO:34), CLκ-Y⁸⁴A (SEQ IDNO:35), and CLκ-R¹⁰³A (SEQ ID NO:36) were also mutated to Ala. The dataof CLκ-D⁴³A and CLκ-H⁸¹A are discussed in Example 14.

The L⁷³A mutant was introduced to 2.12.1.fx CLκ using the three wayligation method. A primer specific to the 5′ end of 2.12.1.fx-LC(2.12.1.fx.LC.FOR: SEQ ID NO:85) and a reverse primer containing thedesired L⁷³A mutation (L181A.REV: SEQ ID NO:88) were used to PCR thefirst half of the 2.12.1.fx-LC using 2.12.1.fx-LC DNA as the PCRtemplate. This PCR fragment was then digested using restriction enzymesBglII and BsaI. A forward primer containing CLκ-L⁷³A mutation(L181A.FOR: SEQ ID NO:87) paired with the reverse primer specific to the3′ end of 2.12.1.fx-LC (2.12.1.fx.LC.REV: SEQ ID NO:86) were used to PCRamplify the second half of 2.12.1.fx-LC DNA fragments carrying mutationusing 2.12.1.fx-LC DNA as the PCR template. This PCR fragment was thendigested using restriction enzymes BsaI and NheI. The two restrictionenzyme digested PCR fragments were ligated with a modified p2.12.1.fxP4plasmid (Invitrogen®) cut with BglII and NheI. The insert sequence wasconfirmed by DNA sequencing. 2.12.1.fx-[CLκ-L⁷³A] (i.e. comprising SEQID NO:28) was transiently expressed in HEK 293 cells, and purified usingprotein A affinity column. The purified mAbs were characterized usingMS.

The CLκ-V⁴²A and CLκ-K⁷⁵A mutants were generated by overlap PCR.Mutations were introduced by oligonucleotide primers. Primer specific tothe 5′ end of 2.12.1.fx-LC (2.12.1.fx.LC.FOR) paired a reverse primercarrying the desired mutation, and a forward primer carrying the desiredmutation paired with the reverse primer specific to the 3′ end of2.12.1.fx light chain (2.12.1.fx.LC.FOR) were used to PCR amplify2.12.1.fx-LC DNA fragments using 2.12.1.fx-LC as template. These two PCRproducts were mixed as templates; 2.12.1.fx-LC forward primer andreverse primer were used in overlap PCR reaction to amplify the fulllength 2.12.1.fx-LC DNA with desired mutation. The PCR was then digestedwith restriction enzyme BglII and NheI. The digested PCR was ligatedwith a modified p2.12.1.fxP4 plasmid (Invitrogen®) cut with BglII andNheI. The insert sequence was confirmed by DNA sequencing. The mutatedmAbs were transiently expressed in HEK 293 cells, and purified usingprotein A affinity column. The purified mAbs were characterized usingMS.

The other mutants were generated on 2.12.1.fx-LC following protocolsdescribed in QuickChange site-directed mutagenesis kit (Stratagene®).Mutations were introduced by oligonucleotide primers and confirmed byDNA sequencing. The mutated mAbs were transiently expressed in HEK 293cells, and purified using protein A affinity column. The purified mAbswere characterized using MS.

2.12.1.fx and 2.12.1.fx mutants (1 mg reaction size) were adjusted 18mg/ml to pH 7.7 with a phosphate buffer to a final concentration of 0.06M sodium phosphate. [PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in apropylene glycol solution to 10 mg/ml. The peptide/linker was added tothe antibody at a molar ratio of 4.3:1 and allowed to react for 2 hrs atroom temperature.

Table 54 compares the conjugation profile of 2.12.1.fx-[PEG₅-K¹¹-SEQ:27]with 2.12.1.fx-[CLκ-mutants]-[PEG₅-K¹¹-SEQ:27]. The conjugation profileof 2.12.1.fx-[PEG₅-K¹¹-SEQ:27] occurs as a distribution between 0-4peptide additions with the largest form being 2 peptide additions. Theprofile changes when the residues are mutated to Ala in the scaffoldprotein; the average number of [PEG₅-K¹¹-SEQ:27] additions eitherdecreased (CLκ-V⁴²A, CLκ-L⁴⁶A, CLκ-S⁷⁴A, CLκ-Y⁷⁸A and CLκ-Y⁸⁴A) orincreased (CLκ-Q⁴⁷A, CLκ-N⁵⁰A and CLκ-D⁷⁷A/E⁷⁹A double mutants) comparedto their corresponding 2.12.1.fx-[PEG₅-K¹¹-SEQ:27] controls. Whencomparing the conjugation profile of CLκ-D⁷⁷A/E⁷⁹A with CLκ-E⁷⁹A, thesignificant increase of average [PEG₅-K¹¹-SEQ:27] additions to theantibody is mainly contributed by the CLκ-D⁷⁷A mutation.

The extent of [PEG₅-K¹¹-SEQ:27] conjugation was examined separately onthe light and heavy chains of 2.12.1.fx and 2.12.1.fx-[CLκ-mutants]. TheMACs were denatured and disulfide bonds were reduced using guanidinehydrochloride and dithiothreitol. The resulting free light and heavychains were analyzed using LCMS to determine the conjugation profile oneach. Table 54 demonstrates that the 1CA on the light chain of2.12.1.fx-[CLκ-Q⁴⁷A] and —[CLκ-N⁵⁰A] are higher than 2.12.1.fx. Theaverage CAs are 0.84 and 0.85 compared to 0.78 of the 2.12.1.fxantibody. Both CLκ-Q⁴⁷A and CLκ-N⁵⁰A mutants have over 70% 1 CA comparedto the 59% 1 CA of the 2.12.1.fx wild type antibody. In addition, theunconjugated light chain levels of these two mutants were reduced from31% of the wild type antibody to 22% and 19%. The V⁴²A had reduced levelof light chain conjugation. The average light chain CA is 0.45 with 59%unconjugated light chain and 37% 1CA. The % of 1-LC % relative to therespective WT run is shown in the right column, as described in Table54.

Conjugation of CLκ-V⁴²A, CLκ-Q⁴⁷A and CLκ-N⁵⁰A to [PEG₅-K¹¹-SEQ:27] wererepeated, and the results are shown at the bottom of the table. Theelevated levels of light chain conjugation in CLκ-Q⁴⁷A and CLκ-N⁵⁰A andreduced light chain conjugation in CLκ-V⁴²A were confirmed by bothintact and reduced LC-MS analysis. Overall, the conjugation datasuggests that CLκ-V⁴², CLκ-D⁴³ and CLκ-H⁸¹ all have an impact on for PFPdirectional conjugation at CLκ-K⁸⁰.

TABLE 54 Conjugation analysis of 2.12.1.fx variants conjugated to [SEQ:27-K¹¹-PEG5], showing amino acid mutants within 10 Ås of light chainK⁸⁰. Ab % CA shows % conjugations additions per antibody, followed bythe average CA per antibody. Reduced light and heavy chain analysis alsoshown, with respective average CA per chain. The % of 1-LC % relative tothe respective WT run is shown in the right column, as described inTable 53. AB % CA Avg. LC % CA Avg. HC % CA Avg. 1LC Ab 0 1 2 3 4 CA 0 12 CA 0 1 CA WT % WT 5 40 43 10 2 1.63 31 59 9 0.78 90 10 0.1 K⁴¹A 6 3249 10 2 1.70 28 65 7 0.78 90 10 0.1 110 V⁴²A 26 45 21 8 1.11 59 37 40.45 90 10 0.1 63 N⁴⁴A 9 37 40 10 4 1.6 31 63 6 0.75 93 7 0.07 107 L⁴⁶A14 42 35 9 1.4 35 62 3 0.68 95 5 0.05 105 Q⁴⁷A 6 27 53 9 4 1.78 22 73 50.84 95 5 0.05 124 S⁴⁸A 6 34 46 9 4 1.72 34 59 7 0.73 93 7 0.07 100 N⁵⁰A4 23 56 13 4 1.89 19 76 4 0.85 95 5 0.05 129 L⁷³A 12 36 33 13 7 1.69 4155 3 0.62 87 13 0.13 93 S⁷⁴A 11 42 39 7 1.43 35 61 5 0.7 96 4 0.04 103K⁷⁵A 12 38 41 9 1.48 35 62 3 0.68 93 7 0.07 105 D⁷⁷A- 3 7 71 15 4 2.1 587 8 1.04 95 5 0.05 147 E⁷⁹A V⁸³A- 9 35 39 11 6 1.7 33 61 6 0.73 86 140.14 103 WT 2 23 49 22 4 2.03 34 60 5 0.71 81 19 0 E⁷⁹A 6 13 51 24 62.12 21 73 6 0.86 85 15 0 122 R¹⁰³A 4 18 51 20 6 2.06 23 70 7 0.83 82 180 117 WT 1 17 51 25 5 2.16 14 77 9 0.96 84 16 0.16 D⁷⁷A 4 6 60 23 7 2.230 86 13 1.13 92 8 0.08 112 V⁴²A 13 28 29 21 9 1.86 49 42 9 0.61 86 140.14 55 Q⁴⁷A 6 7 58 21 9 2.2 8 85 7 0.99 91 9 0.09 110 N⁵⁰A 7 8 51 25 92.2 10 81 9 0.99 90 10 0.1 105

Example 28 Analysis of CLκ-D⁴³A and CLκ-H⁸¹A Mutants

In order to determine whether the charge, hydrogen bond or the size ofCLκ-D⁴³ are important to the CLκ-K⁸⁰ directional conjugation, CLκ-D⁴³was mutated to CLκ-D⁴³E (SEQ ID NO:107), CLκ-D⁴³N (SEQ ID NO:108) andCLκ-D⁴³L (SEQ ID NO:109) respectively. The mutants were generated on2.12.1.fx antibody light chain following protocols described inQuickChange site-directed mutagenesis kit (Stratagene®). Mutations wereintroduced by oligonucleotide primers and confirmed by DNA sequencing.The mutated mAbs were transiently expressed in HEK 293 cells, andpurified using protein A affinity column. The purified mAbs werecharacterized using MS.

Similarly, in order to assess the role of CLκ-H⁸¹, the following mutantversions of the test antibody 2.12.1.fx were assessed: CLκ-H⁸¹N (SEQ IDNO:110), CLκ-H⁸¹Q (SEQ ID NO:111), CLκ-H⁸¹Y (SEQ ID NO:112), CLκ-H⁸¹W(SEQ ID NO:113) and CLκ-H⁸¹F (SEQ ID NO:114).

2.12.1.fx antibody and 2.12.1.fx-[CLκ-mutant]-antibodies (1 mg reactionsize) were adjusted 18 mg/ml to pH 7.7 with a phosphate buffer to afinal concentration of 0.06 M sodium phosphate. [PFP-PEG₅-K¹¹-SEQ:27]was reconstituted in a propylene glycol solution to 10 mg/ml. Thepeptide/linker was added to antibody at a molar ratio of 4.3:1 andallowed to react for 2 hrs at RT.

CLκ-D⁴³N has the similar overall conjugation and light chain levels(Table 55) compared to the wild type antibody. CLκ-D⁴³E and CLκ-D⁴³Lshowed reduced overall conjugation level light chain conjugation level.

CLκ-H⁸¹N, CLκ-H⁸¹Q, CLκ-H⁸¹Y, Y CLκ-H⁸¹W and CLκ-H⁸¹F mutants showedreduced overall conjugation level light chain conjugation level,suggesting that the imidazole ring is required for the PFP directionalconjugation. The conjugation reaction does not involve the π-stackinginteraction nor the H-bonds formed with Nε2 or Nδ1 of the imidazolering.

TABLE 55 2.12.1.fx variants conjugated to [PEG₅-K¹¹-SEQ: 27] (WT is2.12.1.1fx). Ab % CA shows % conjugations additions per antibody,followed by the average CA per antibody. Reduced light and heavy chainanalysis also shown, with respective average CA per chain. The % of 1-LC% relative to the respective WT run is shown in the right column, asdescribed in Table 53. Ab % CA Avg LC % CA Avg HC % CA Avg 1LC Ab 0 1 23 4 CA 0 1 2 CA 0 1 2 CA WT % WT 2 23 49 22 4 2.03 34 60 5 0.71 81 19 00.19 D⁴³N 7 24 39 21 8 2.00 34 59 7 0.73 84 16 0 0.16 98 D⁴³L 14 33 3419 0 1.57 55 40 5 0.50 74 26 0 0.26 67 D⁴³E 9 33 37 17 4 1.75 44 48 80.63 74 26 4 0.34 80 H⁸¹N 32 41 20 7 0 1.04 84 16 0 0.16 70 26 5 0.35 27H⁸¹Q 29 40 21 11 0 1.14 82 17 1 0.19 73 27 0 0.27 28 H⁸¹Y 27 40 24 8 01.14 80 20 0 0.20 70 26 4 0.35 33 H⁸¹W 29 45 19 8 0 1.05 85 15 0 0.15 6926 5 0.36 25 H⁸¹F 13 41 30 15 0 1.48 79 21 0 0.21 70 30 0 0.30 35

Example 29 2.12.1.fx-[CLκ-D⁷⁷A] Conjugation Using Different ReactiveEsters

2.12.1.fx and 2.12.1.fx-[CLκ-D⁷⁷A] were conjugated to [PEG₅-K¹¹-SEQ:27]using different reactive esters (see Examples 18 and 19) (results shownin Table 56). For all of the different activated esters, the2.12.1.fx-[CLκ-D⁷⁷A] mutant gave a higher level of intact average CAupon conjugation compared to the wt 2.12.1.fx. Another clear trend wasthat the level of 0 and 1 CA in the wild type 2.12.1.fx was markedlydecreased in the 2.12.1.fx-[CLκ-D⁷⁷A] mutant for each of the activatedesters, and that the level of 2 CA was increased in each case for mostactivated esters, except for Z9.

The results of the reduced LC/HC analyses showed a further obvious trendcomparing the 2.12.1.fx and 2.12.1.fx-[CLκ-D⁷⁷A] conjugation results. Ineach case, the degree of underivatized LC decreased, substantially insome cases. This was accompanied by a concomitant increase in the levelof 1 CA on the LC, again for each different active ester, so thatoverall the average amount of derivatization on the LC increased. Thegeneral trend for the LC was that the amount of 1CA increased by theamount that 0CA decreased, as the amount of 2CA present in each case wasessentially unchanged.

In considering the HC, another trend was apparent in that the alreadylow amount of 1CA derivatization for each active ester was furtherdecreased. The outlier in this trend was Z9, the only non-phenolicester. This ester shows little of the directional conjugation effecttowards CLκ-K⁸⁰ compared to the other phenolic esters and the levels ofboth LC and HC derivatization are similar, with only a minor improvementin directionality imparted by the 2.12.1.fx-[CLκ-D⁷⁷A] mutant. Overall,the 2.12.1.fx-[CLκ-D⁷⁷A] mutant provides clear evidence of improveddirectional LC conjugation compared to native 2.12.1.fx for a range ofactivated esters

TABLE 56 Analysis of 2.12.1.fx.-[CLκ-D⁷⁷A] conjugation to [PEG5-K¹¹-SEQ:27] using different reactive esters (see Examples 26 and 27). Ab % CAshows the overall % of conjugation additions per antibody, with reducedlight chain and heavy chain analysis also shown (LC % CAN, HC % CA). andΔ indicates the difference between the WT and D¹⁸⁵A mutant results forAb % CA. The % of 1-LC % relative to the respective WT run is shown inthe right column, as described in Table 53. Ab % CA Avg LC % Avg. Avg.1LC Z# Ab 0 1 2 3 4 CA Δ 0 1 2 CA 0 1 2 CA WT % 1 WT 1 17 51 25 5 2.160.07 14 77 9 0.96 84 16 0.16 D⁷⁷A 4 6 60 23 7 2.23 0 86 13 1.13 92 80.08 112 2 WT 15 43 33 9 1.36 0.72 49 49 3 0.54 84 16 0.16 D⁷⁷A 7 14 5319 8 2.09 16 81 3 0.87 90 10 0.1 33 10 WT 23 44 26 7 1.18 0.73 60 38 20.42 81 19 0.19 D⁷⁷A 6 27 43 18 6 1.91 29 67 4 0.74 89 11 0.11 176 3 WT7 32 39 18 5 1.82 0.43 44 48 7 0.63 79 21 0.21 D⁷⁷a 6 11 46 25 12 2.2512 79 9 0.97 90 10 0.1 165 6 WT 15 46 30 9 1.34 0.71 41 52 7 0.66 88 120.12 D⁷⁷a 6 21 44 20 9 2.05 18 73 8 0.9 93 7 0.07 140 9 WT 7 29 35 21 81.94 0.26 57 34 9 0.51 56 34 10 0.54 D⁷⁷a 10 19 29 27 15 2.20 47 44 90.63 61 32 7 0.46 129

Example 30 Trastuzumab (Herceptin®) Conjugation

In order to confirm that the improved directional conjugation to CLκ-K⁸⁰caused by CLκ-D⁷⁷ mutation can be applied to other antibodies comprisingCLκ, D⁷⁷A mutation was also inserted to the CLλ of trastuzumab (hTrast).Trastuzumab light chain and heavy chain DNA were synthesized based onthe amino acid sequences on Drug Bank, Accession Number DB00072(BIOD00098, BTD00098).

hTrast-[CLκ-D⁷⁷A] mutant was generated in two steps. First, D⁷⁷Amutation was generated on an antibody light chain following protocolsdescribed in QuickChange site-directed mutagenesis kit (Stratagene®).Mutations were introduced by oligonucleotide primers and confirmed byDNA sequencing. The VL of trastuzumab was ligated with the CL of theantibody with D⁷⁷A mutation. Primer pair TRAST.VL.FOR (SEQ ID NO:89) andTRAST.VL.REV (SEQ ID NO:90) were used to amplify trastuzumab VL. The PCRfragment was digested with BglII and BsaI. Primer pairTRAST.CL.D185A.FOR (SEQ ID NO:91) and TRAST.CL.D185.A.REV (SEQ ID NO:92)were used to amplify CL with D⁷⁷A mutation. The resulting PCR fragmentwas digested with BsaI and NheI. Restriction enzyme digested PCRfragments were ligated with a modified p2.12.1.fxP4 plasmid(Invitrogen®) cut with BglII and NheI. The insert sequence was confirmedby DNA sequencing. The mutated mAb was transiently expressed in HEK 293cells, and purified using protein A affinity column. The purified mAbwas characterized using MS.

Trastuzumab and hTrast-[CLκ-D⁷⁷A] (1 mg reaction size) were adjusted 18mg/ml to pH 7.7 with a phosphate buffer to a final concentration of 0.06M sodium phosphate. [PFP-PEG₅-K¹¹-SEQ:27] was reconstituted in apropylene glycol solution to 10 mg/ml. The peptide/linker was added toantibody at a molar ratio of 4.3:1 and allowed to react for 2 hrs at RT.

Table 57 compares the conjugation profile oftrastuzumab-[PEG₅-K¹¹-SEQ:27] with hTrast-[CLκ-D⁷⁷A]-[PEG₅-K¹¹-SEQ:27].The conjugation profile of trastuzumab -[PEG₅-K¹¹-SEQ:27] occurs as adistribution between 0-4 peptide additions with the average number ofpeptide additions being 1.75. The profile changes following the D⁷⁷Amutation; the average number of peptide additions rises to 2.18 andsignificantly less overall levels of 0 and 1 peptide addition isobserved. This result suggests that the single point mutation CLκ-D⁷⁷Ahas the effect of increasing the overall conjugation to the scaffold, asseen in the test antibody 2.12.1.fx.

The reduced light and heavy chain analysis demonstrates that the averageconjugation is higher on the light chain of hTrast-[CLκ-D⁷⁷A] thanunmodified trastuzumab; the average light chain conjugate addition valuefor hTrast-[CLκ-D⁷⁷A] is 1.01 compared to 0.70 for trastuzumab. Inaddition, unconjugated light chain is significantly reduced inhTrast-[CLκ-D⁷⁷A]. Conjugation on the heavy chain is observed at asignificantly lower level. The majority of observed heavy chain for bothtrastuzumab and hTrast-[CLκ-D⁷⁷A] is unconjugated; this is especiallytrue in the case of hTrast-[CLκ-D⁷⁷A] heavy chain. These results suggestthat the CLκ-D⁷⁷A mutation alters the light chain to make itsignificantly more susceptible to conjugation.

TABLE 57 Analysis of conjugation of [PEG₅-K¹¹-SEQ: 27] to Abstrastuzumab (WT) and hTrast-[CLκ-D⁷⁷A]. Rep = replicate. AvReps is theaverage of the results of the three replicate experiments, with thestandard deviation shown beneath (StdDev). Ab % CA shows % conjugationsadditions per antibody, followed by the average CA per antibody. Reducedlight and heavy chain analysis also shown. Ab Ab % CA Avg. LC % CA Avg.HC % CA Avg. WT 0 1 2 3 4 CA 0 1 2 CA 0 1 CA Rep1 6 33 42 15 5 1.80 3565 ND 0.65 85 15 0.15 Rep2 7 34 39 14 6 1.79 26 74 ND 0.74 84 16 0.16Rep3 9 38 38 11 5 1.65 30 70 ND 0.7 82 18 0.18 Av. Rep 7 35 40 13 5 1.7530 70 0.70 84 16 0.16 StdDev 2 3 2 2 1 0.08 5 5 0.05 2 2 0.02 D⁷⁷A 5 923 0.99 94 6 0.06 Rep1 4 5 66 20 6 2.19 1 94 5 1.04 91 9 0.09 Rep2 3 5 6521 6 2.22 3 95 2 0.99 94 6 0.06 Rep3 3 8 69 17 4 2.12 3 94 3 1.01 93 70.07 AvRep 3 6 67 19 5 2.18 2 2 2 0.03 2 2 0.02 StdDev 1 2 2 2 1 0.05 592 3 0.99 94 6 0.06

Example 31 Conjugation of Trastuzumab with MMAD

Table 58 compares the conjugation profile of trastuzumab -[PEG₅-MMAD](Auristatin derivative) with hTrast-[CLκ-D⁷⁷A]-[PEG-MMAD].

The conjugation profile of trastuzumab-[PEG₅-MMAD] occurs as adistribution between 0-4 conjugations per antibody with the largest formbeing 2 conjugations and the average number of conjugations is 1.65.When CLκ-D⁷⁷A is mutated, the average number of conjugations rises to2.00 and significantly less overall levels of 0 and 1 MMAD addition isobserved. This result suggests that the single point mutation CLκ-D⁷⁷Ahas the effect of increasing the overall conjugation to the scaffold andthat this technology is applicable to an antibody toxin conjugationmodel.

Reduced heavy and light chain analysis demonstrates that the averageconjugation is higher on the light chain of hTrast-[CLκ-D⁷⁷A] thanunmodified trastuzumab; the average light chain conjugate addition valuefor hTrast-[CLκ-D⁷⁷A] is 0.88 compared to 0.56 for trastuzumab. Inaddition, unconjugated light chain is significantly reduced inhTrast-[CLκ-D⁷⁷A]. Conjugation on the heavy chain is observed at asignificantly lower level. The majority of observed heavy chain for bothtrastuzumab and hTrast-[CLκ-D⁷⁷A] is unconjugated; this is especiallytrue in the case of hTrast-[CLκ-D⁷⁷A] heavy chain. These results suggestthat the CLκ-D⁷⁷A mutation alters the light chain to make itsignificantly more susceptible to conjugation.

TABLE 58 Analysis of [PEG₅-MMAD] conjugation to trastuzumab (WT) andhTrast-[CL_(K)-D⁷⁷A], also showing reduced LC and HC analysis. Ab % CAshows % conjugations additions per antibody, followed by the average CAper antibody. Reduced light and heavy chain analysis also shown. The %of 1-LC % relative to the respective WT run is shown in the rightcolumn, as described in Table 53. hTrast 1LC conjugated Percent CA Avg.LC % CA Avg. HC % CA Avg. WT to MMAD 0 1 2 3 4 CA 0 1 2 CA 0 1 CA % WT 835 42 13 2 1.65 45 54 1 0.56 76 23 0.23 D⁷⁷A 1 16 65 16 1 2.00 11 880.88 84 14 0.14 163

Example 32 Ability of Conjugated Trastuzumab to Bind Targets

The ability of trastuzumab and hTrast-[CLκ-D⁷⁷A], unconjugated andconjugated to either [PEG₅-K¹¹-SEQ:27] or [PEG₅-MMAD] and to bind to theHer2 receptor was studied using a Her2 binding ELISA assay. Half wellELISA plates were coated with 1 ug/ml of Fc-ErbB2 fusion protein in PBSand incubated at 4° C. overnight. Plates were washed 3 with KPL washbuffer and subsequently blocked with Superblock for 1 hr at RT. 10×serial dilutions of samples were prepared in Superblock, with a topconcentration of 100 μg/ml. Samples were added to wells and plates wereincubated for 1 hr at RT. Plates were washed 3× with KPL wash buffer.Bound samples were detected by incubating with a 1:1000 dilution ofanti-human Fab-HRP secondary antibody for 1 hr at RT. Plates were againwashed 3× with KPL wash buffer and HRP was detected with TMB substrate.The reaction was stopped with 2M H₂SO₄ and OD was measured at 450 nm ona Spectramax plate reader.

FIGS. 9A and 9B demonstrate that commercial trastuzumab, trastuzumabgenerated from the available sequence, and hTrast-[CLκ-D⁷⁷A], as well astrastuzumab and hTrast-[CLκ-D⁷⁷A] when bound to either of[PEG₅-K¹¹-SEQ:27] or [PEG₅-MMAD] each display similar Her2 bindingcharacteristics. These result suggest that conjugation, primarily atCLκ-K⁸⁰, does not significantly interfere with the receptor bindingfunction of the native antibody.

Example 33 Comparison of PFP and NHS Conjugation Strategies

Trastuzumab was conjugated to [PEG₅-MMAD] using two separate strategies:directional conjugation to CLκ-K⁸⁰ using PFP ester (Z1) as the Z* group(generating trastuzumab-[5PEG-MMAD]), or NHS (Z13; generatingtrastuzumab-[MMAD]_(n)), which resulted in a wider conjugation patternacross the antibody, and dosed to rats to compare the tolerability ofthe antibody drug conjugates. Both conjugates were given as 10, 30 and100 mg/kg single bolus doses. All animals dosed at 10, and 30 mg/kgdoses of both conjugates during the one week study period survivedwithout significant body weight loss. However, the 100 mg/kg dose groupshowed a clear difference between random conjugation (Z13) and siteselective conjugation to CLκ-K⁸⁰ (Z1). Greater than 50% of the animalsin 100 mg/kg dose of the random conjugate (NHS conjugation) died withinthe one week study period while all animals in the 100 mg/kg dose of thesite selective conjugate (PFP conjugation) survived without significantbody weight loss (Table 59). This may suggest that preferentialconjugation at CLκ-K⁸⁰ may provide a more reliable mechanism forconjugation of Effector Moieties then traditional ‘random’ approaches,as conjugation on multiple surface lysine residues may give rise toEffector Moieties that have less reliable cleavage and degradationpatterns.

TABLE 59 Site selective conjugation of toxin improves the tolerabilityof the antibody drug conjugates. Comparison of tolerability oftrastuzumab -[PEG₅-MMAD] in rats after conjugation using Z1 and Z13 asZ* groups. Conjugate Conjugation type Dose (mg/Kg) % SurvivalTrastuzumab-[PEG₅- PFP 10 100 MMAD] 30 100 100 100Trastuzumab-[MMAD]_(n) NHS 10 100 30 100 100 50

Example 34 h38C2 Conjugated with Toxin and Cleavable Linker

A targeting peptide was conjugated to the combining site of a CLκ-D⁷⁷Amutated version of catalytic antibody h38C2 (HC=SEQ ID NO:65 and LC=SEQID NOs:37 and 67) using a linker of the formula P-Q-W as hereindescribed, with a β-lactam group as the W group to form a covalentattachment with the side chain of K⁹⁹ of SEQ ID NO:65. This conjugatedantibody was then further conjugated with the PFP-activated ester of anexemplary Auristatin-based toxin attached to a valine-citrullinep-aminobenzyl carbamate cleavable linker ([PFP-PEG₂-ValCitABC-TOXIN]).

A distribution of conjugates was observed with primarily 2-3 toxins perantibody scaffold (Table 60). In vitro cytotoxicity assays of thisconjugate demonstrated potent anti-proliferative effects in AU565 celllines (IC₅₀=0.4 nM) and OVCAR5 cell lines (IC₅₀=0.2 nM).

TABLE 60 Conjugation profile of h38C2 conjugated to [PFP-PEG₂-ValCitABC-TOXIN]. Conjugation Additions (CA) (%) Avg 0 1 2 3 4 5 CAPFP-PEG₂-ValCitABC-TOXIN 4 8 31 29 18 10 2.8

Example 35

A structural analog of PFP, with a trifluoromethyl group replacing thepara-fluorine atom, was used to make a derivative Z* group;2,3,5,6-tetrafluoro-4-(trifluoromethyl)phenyl (Z16):

2,3,5,6-tetrafluoro-4-(trifluoromethyl)phenyl

This was used to generate a Z16-PEG₅ linker, which was conjugated to thetest peptide SEQ ID NO:27, and tested in conjugation with the testantibody 2.12.1.fx. In contrast to other Z* groups tested, thisderivative gave a conjugate with a slightly higher level of conjugationfor the native 2.12.1.fx compared to 2.12.1.fx-[CLκ-D⁷⁷A], but bothlevels of intact conjugation were higher for the conjugate using the Z16group than the corresponding PFP (Z1) analogs (around 10% increase inoverall average CA compared to Z1). Using Z16, both native 2.12.1.fx and2.12.1.fx-[CLκ-D⁷⁷A] conjugations showed an equivalent level of 1CA, andthis was lower than that observed for native 2.12.1.fx conjugated with[PFP-PEG₅-K¹¹-SEQ:27]: for other conjugations, the level of 1CA istypically reduced in the D⁷⁷A compared to the corresponding nativeantibody. Overall, the results suggest that the leaving group D16 ismore reactive than Z1 (PFP) (Table 61).

The Z16 leaving group shows roughly equivalent derivatization for boththe native 2.12.1.fx and 2.12.1.fx-[CLκ-D⁷⁷A] antibodies and the amountof underivatized LC is small in both cases. Again the overall level ofLC and HC derivatization is increased using Z*16 compared to Z1. Theleaving group Z16 appears a more reactive ester than PFP, but it ispossible that the CF₃ group is providing an additional interaction nearthe CLκ-K⁸⁰ region that is also driving reactivity and preferentialderivatization of the LC.

TABLE 61 Analysis of 2.12.1.fx and 2.12.1.fx.-[CL_(K)-D⁷⁷A] conjugationto [PEG₅-K¹¹-SEQ:27] using different reactive Z* groups Z1 and Z16. AvgHC % Avg 1LC Z 2.12. Ab % CA Avg LC % CA CA- CA CA- WT * 1.fx 0 1 2 3 4CA Δ 0 1 2 LC 0 1 HC % 1 WT 1 17 51 25 5 2.16 14 77 9 0.96 84 16 0.16 1D⁷⁷A 4 6 60 23 7 2.23 0.07 0 86 13 1.13 92 8 0.08 112 16 WT 4 4 44 36 122.48 5 83 12 1.07 81 19 0.19 16 D⁷⁷A 9 9 31 33 18 2.43 0.05 1 79 20 1.289 11 0.11 95 Ab % CA shows the overall % of conjugation additions perantibody, with reduced light chain and heavy chain analysis also shown(LC % CA, HC % CA). Δ indicates the difference between the WT and D¹⁸⁵Amutant results for Ab % CA. The % of 1-LC % relative to the respectiveWT run is shown in the right column, as described in Table 53.

Example 36 Synthesis of Toxin 0101 Experimental for Toxin 0101 (#54 inthe Schematic) Preparation of2-Methylalanyl-N-[(3R,4S,5S)-3-methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-2-methyl-3-oxo-3-{[(1S)-2-phenyl-1-(1,3-thiazol-2-yl)ethyl]amino}propyl]pyrrolidin-1-yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide(#54)

Step 1 Synthesis ofN-[(9H-fluoren-9-ylmethoxy)carbonyl]-2-methylalanyl-N-[(3R,4S,5S)-3-methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-2-methyl-3-oxo-3-{[(1S)-2-phenyl-1-(1,3-thiazol-2-yl)ethyl]amino}propyl]pyrrolidin-1-yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide(#53)

According to general procedure D (below), from #32 (2.05 g, 2.83 mmol, 1eq.) in dichloromethane (20 mL, 0.1 M) and N,N-dimethylformamide (3 mL),the amine #19((2R,3R)-3-methoxy-2-methyl-N-[(1S)-2-phenyl-1-(1,3-thiazol-2-yl)ethyl]-3-[(2S)-pyrrolidin-2-yl]propanamide,trifluoroacetic acid salt) (2.5 g, 3.4 mmol, 1.2 eq.), HATU (1.29 g,3.38 mmol, 1.2 eq.) and triethylamine (1.57 mL, 11.3 mmol, 4 eq.) wassynthesized the crude desired material, which was purified by silica gelchromatography (Gradient: 0% to 55% acetone in heptane), producing #53(2.42 g, 74%) as a solid. LC-MS: m/z 965.7 [M+H⁺], 987.6 [M+Na⁺],retention time=1.04 mins; HPLC (Protocol A): m/z 965.4 [M+H⁺], retentiontime=11.344 mins (purity >97%); ¹H NMR (400 MHz, DMSO-d₆), presumed tobe a mixture of rotamers, characteristic signals: δ 7.86-7.91 (m, 2H),[7.77 (d, J=3.3 Hz) and 7.79 (d, J=3.2 Hz), total 1H], 7.67-7.74 (m,2H), [7.63 (d, J=3.2 Hz) and 7.65 (d, J=3.2 Hz), total 1H], 7.38-7.44(m, 2H), 7.30-7.36 (m, 2H), 7.11-7.30 (m, 5H), [5.39 (ddd, J=11.4, 8.4,4.1 Hz) and 5.52 (ddd, J=11.7, 8.8, 4.2 Hz), total 1H], [4.49 (dd,J=8.6, 7.6 Hz) and 4.59 (dd, J=8.6, 6.8 Hz), total 1H], 3.13, 3.17, 3.18and 3.24 (4 s, total 6H), 2.90 and 3.00 (2 br s, total 3H), 1.31 and1.36 (2 br s, total 6H), [1.05 (d, J=6.7 Hz) and 1.09 (d, J=6.7 Hz),total 3H].

Step 2 Synthesis of2-methylalanyl-N-[(3R,4S,5S)-3-methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-2-methyl-3-oxo-3-{[(1S)-2-phenyl-1-(1,3-thiazol-2-yl)ethyl]amino}propyl]pyrrolidin-1-yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide(#54)

According to general procedure A (below), from #53 (701 mg, 0.726 mmol)in dichloromethane (10 mL, 0.07 M) was synthesized the crude desiredmaterial, which was purified by silica gel chromatography (Gradient: 0%to 10% methanol in dichloromethane). The residue was diluted withdiethyl ether and heptane and was concentrated in vacuo to afford #54(406 mg, 75%) as a white solid. LC-MS: m/z 743.6 [M+H⁺], retentiontime=0.70 minutes; HPLC (Protocol A): m/z 743.4 [M+H⁺], retentiontime=6.903 minutes, (purity >97%); ¹H NMR (400 MHz, DMSO-d₆), presumedto be a mixture of rotamers, characteristic signals: 8 [8.64 (br d,J=8.5 Hz) and 8.86 (br d, J=8.7 Hz), total 1H], [8.04 (br d, J=9.3 Hz)and 8.08 (br d, J=9.3 Hz), total 1H], [7.77 (d, J=3.3 Hz) and 7.80 (d,J=3.2 Hz), total 1H], [7.63 (d, J=3.3 Hz) and 7.66 (d, J=3.2 Hz), total1H], 7.13-7.31 (m, 5H), [5.39 (ddd, J=11, 8.5, 4 Hz) and 5.53 (ddd,J=12, 9, 4 Hz), total 1H], [4.49 (dd, J=9, 8 Hz) and 4.60 (dd, J=9, 7Hz), total 1H], 3.16, 3.20, 3.21 and 3.25 (4 s, total 6H), 2.93 and 3.02(2 br s, total 3H), 1.21 (s, 3H), 1.13 and 1.13 (2 s, total 3H), [1.05(d, J=6.7 Hz) and 1.10 (d, J=6.7 Hz), total 3H], 0.73-0.80 (m, 3H).

General Procedure A:

Fmoc removal using diethylamine. To a solution of the Fmoc-containingcompound in dichloromethane was added an equal volume of diethylamine.Reaction progress was monitored by LC-MS (or HPLC or TLC); the reactionwas usually completed within three hours. Solvents were removed invacuo, and the residue was azeotroped three times with heptane. Theresidue was then diluted with dichloromethane and a small amount ofmethanol before being reduced down onto silica and purified bychromatography on silica gel, eluting with methanol in dichloromethaneto afford the desired material.

General Procedure D:

coupling with O-(7-azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluroniumhexafluorophosphate (HATU). To a stirring solution of the amine (1 eq.)and acid (1.1 eq.) in dichloromethane: N,N-dimethylformamide (4:1, 0.3 Min amine) was added HATU (1.2 eq.) followed by Et₃N (3 eq.). Reactionprogress was monitored by LC-MS (or HPLC or TLC); the reaction wasusually completed within three hours. Solvents were removed in vacuo.The residue was azeotroped three times with heptane and was diluted witha small amount of ethyl acetate before being reduced down onto silicaand purified by silica gel or reverse phase chromatography.

Example 37 Preparation of MAC Comprising mAb hu08 and Toxin 0101

Hu08 is a human anti-IL-13Rα2 antibody, and is described fully inUS61/723,545, whose contents are herein incorporated by reference. Amutant version of hu08, comprising the CLκ-D⁷⁷A mutation was generatedaccording to standard protocols (hu08-[CLκ-D77A]). Toxin-0101 (#54:Example 36) was conjugated with a cleavable linker to form thestructure:

and then the toxin-linker was conjugated to hu08-[CLκ-D77A] according tothe techniques described herein. The compound hu08-vc-0101 wasgenerated, resulting in non-specific conjugation of multiples ofToxin-0101 on the antibody hu08 via the linker-Toxin-0101 species:

In Vitro Cytotoxicity Assay

Cell lines expressing the IL-13Rα2 antigen and a negative control cellline were cultured with increasing concentrations of hu08-[CLκ-D⁷⁷A].After four days, viability of cultures were assessed. IC₅₀ values werecalculated by logistic non-linear regression and are presented as ngAb/mL.

The data demonstrate that hu08-vc0101 and hu08-[CLκ40, -D⁷⁷A] were botheffective against both of the IL-13Rα2 positive cell lines tested(PC3MM2 and A375), having an IC₅₀ ranging from 2.5 to 7.9 ng Ab/mL(Table 62). Neither hu08-vc0101 nor hu08-[CLκ-D⁷⁷A] were active againstthe IL-13Rα2 negative cell line, H460, and the non-IL-13Rα2 bindingcontrol, hIgG8.84-vc0101, was not active against any of the cell linestested.

TABLE 62 In vitro cytotoxicity assay of hu08-[CLκ-D⁷⁷A] -0101. IC₅₀ (ngAb/mL) ADC Toxin: Ab PC3MM2 A375 H460 hu08-vc-0101 3.2 2.5 3.8 >400000hu08-[CLκ-D⁷⁷A] -0101 1.9 4.9 7.9 >400000 hIgG8.8-vc-01013.7 >400000 >400000 >400000

Subcutaneous Xenograft Models of Cys Mutant ADCs

Female, athymic (nude) mice were injected s.c. with PC3MM2 tumor cells.Mice with staged tumors, approximately 0.1 to 0.3 g (n=8 to 10mice/treatment group) were administered intravenously q4d×4 with normalsaline (vehicle) or MAC-0001. Compounds were dosed based on Ab content.Tumors were measured at least once a week and their size (mm2+/−SEM) iscalculated as mm³=0.5×(tumor width²)×(tumor length). The data in Table63 indicate that hu08-[CLκ-D⁷⁷A]-0101 inhibits the growth of PC3MM2xenografts.

TABLE 63 Dose PC3MM2 xenograft, tumor volume (mm³ ± SEM) single Day DayDay Day Day Day Day Day Day Day ADC dose 0 5 8 12 15 20 30 41 55 77Vehicle 0 325 590 782 1140 GT GT GT GT GT GT ± 9  ± 41 ± 79  ± 142hu08-[CL_(K)- 1.5 328 393 352 432 556 732 D⁷⁷A]-0101 ± 49 ± 96 ± 106 ±124 ± 236 ± 305 GT GT GT GT hu08-vc- 1.5 333 431 281 299 362 450 956 GTGT GT 0101 ± 12 ± 40 ± 25  ± 32  ± 47  ± 58  ± 166 GT = group terminateddue to large tumor size

Example 38 Trastuzumab MMAD Conjugate Activities

Three trastuzumab conjugates were made: trastuzumab-[5PEG-MMAD],hTrast-[CLκ-D⁷⁷A]-[5PEG-MMAD], and trastuzumab-(MMAD)_(n), where MMADwas connected to a 5PEG linker with Z13 (NHS) as leaving group, andconjugated to trastuzumab without directional conjugation techniques,resulting in non-specific conjugation of MMAD to trastuzumab surfacelysines (see Examples 30-33)

The three mAb conjugates were evaluated in an exploratory toxicity studyin rats in which animals received single intravenous bolus doses of eachADC at 0 (vehicle), 10, 30, and 100 mg/kg (5 male rats/group) and werethen observed for 14 days. Toxicology evaluation included daily clinicalobservations, weekly body weight measurements and clinical pathologyevaluation on the day of necropsy. Animals were euthanized on day 15 andselected tissues were collected for microscopic examination. Inaddition, blood samples were collected from all animals at approximately0.0833 (5 min), 6, 24 (day 2), 48 (day 3), 72 (day 4), 96 (day 5), 168(day 8), and 312 (day 14) hrs post-dose and analyzed forantibody-conjugate and trastuzumab antibody concentrations.

Results

The plasma exposures (based on AUC) were overall similar for all 3conjugates at any given dose. The AUC (0-312) ofhTrast-[CLκ-D⁷⁷A]-[5PEG-MMAD], trastuzumab-[5PEG-MMAD] andtrastuzumab-(MMAD)_(n) at 100 mg/kg were 177000, 174000 and 139000ng·h/mL, respectively. hTrast-[CLκ-D⁷⁷A]-[5PEG-MMAD] andtrastuzumab-[5PEG-MMAD] were clinically well tolerated at all doses.However, trastuzumab-(MMAD)_(n) administration at 100 mg/kg wasassociated with marked clinical signs and premature euthanasia of 1/5rats on Day 8. Other rats from this group had decreased skin turgor anddecreased body weight gain.

Clinical pathology changes were overall similar withhTrast-[CLκ-D⁷⁷A]-[5PEG-MMAD] and trastuzumab-[5PEG-MMAD] and includedin particular mild decreases in red blood cell (RBC) mass (RBC count,hemoglobin and/or hematocrit) at 0 or 30 mg/kg and minimal increases inaspartate aminotransferase (AST) at 100 mg/kg. The RBC mass changes weremore pronounced with trastuzumab-(MMAD)_(n) and were associated withdecreased erythroid cellularity in the bone marrow. Other noteworthytrastuzumab-(MMAD)_(n)-related clinical pathology changes at 100 mg/kgincluded moderate decreases in platelet counts and mild increases inALT, AST, ALP and total bilirubin.

Microscopic findings were overall similar forhTrast-[CLκ-D⁷⁷A]-[5PEG-MMAD] and trastuzumab-[5PEG-MMAD] and includedalveolar histiocytosis/inflammation in the lung, degeneration of smallbile ducts in the liver and increased tingible body macrophages(containing cell debris) in the bone marrow. Increased mitoses inseveral tissues and single cell necrosis in the cornea were consideredpharmacologically mediated effects of tubulin inhibition resulting inmitotic arrest and apoptosis. By contrast, trastuzumab-(MMAD)_(n)administration was associated with more pronounced microscopic tissuealterations, which included tubular degeneration/necrosis andglomerulopathy in the kidney; single cell necrosis, bile ductdegeneration and hyperplasia and centrilobular necrosis/fibrosis in theliver; alveolar histiocytosis/inflammation in the lung; increasedtangible body macrophages, degeneration/decreased numbers ofhematopoietic cells and osteolysis in the bone marrow; decreasedmarginal zone cellularity in the spleen. Of special note, centrilobularfibrosis in the liver in association with disruption of the normallobular architecture was consistent with a reparative change suggestingearlier, more extensive treatment-related hepatocellular damage. Inaddition, pharmacologically mediated increased mitoses and/or singlecell necrosis were observed in several tissues.

In summary, hTrast-[CLκ-D⁷⁷A]-[5PEG-MMAD] and trastuzumab-[5PEG-MMAD]were well tolerated at all doses (10, 30, and 100 mg/kg) anddemonstrated overall similar toxicity profiles. Trastuzumab-(MMAD)_(n)administration led to premature mortality at 100 mg/kg and wasassociated with significant target organ toxicities in the liver,kidney, lung and bone marrow in particular.

Example 39 Modeling of CLκ and CLλ

FIG. 10A depicts an Ig fold of a constant light domain containing a3-stranded β-sheet packed against a 4-stranded β-sheet. The fold isstabilized by hydrogen bonding between the β-strands of each β-sheet, byhydrophobic bonding between residues of opposite β-sheets in theinterior, and by a disulfide bond between the β-sheets. The 3-strandedβ-sheet comprises β-strands C, F, and G, and the 4-stranded β-sheet hasβ-strands A, B, E, and D. The letters A through G denote the sequentialpositions of the β-strands along the amino acid sequence of the Ig fold.Linking each β-strand with the subsequent β-strand is an amino acidconnecting chain that may or may not comprise a turn (NB) or α-helix(E/F) (FIG. 10B).

FIG. 8B plots the secondary structures along the primary sequence of themouse and human CLκ, and the human CLλ. The EF connecting chain betweenβ-strands E and F of the CLκ and CLλ have identical secondary structureand consist of a 5-6 residue α-helical region (CLκ-K⁷⁵-K⁸⁰, andCLλ-P⁷⁶-S⁸¹), followed by a 2-3 amino-acid turn (CLκ-H⁸¹-K⁸² andCLλ-H⁸²-S⁸⁴) (FIGS. 8B and 10). The CD connecting chain brings the sidechain of structurally equivalent aspartic acids (CLκ-D⁵³, CLλ-D⁴⁵) tothe vicinity of the EF chain (approximately 3.5 Å), and allows CLκ-D⁵³interact with the imidazole ring of CLκ-H⁸¹.

Modeling of the CLλ and comparison with the CLκ suggests that CLλ-D⁴⁵cooperates with the imidazole ring of CLλ-H⁸² in the same manner, andthat mutating CLλ-S⁸¹ to CLλ-K⁸¹ recreates a similar local environmentas found on the CLκ, and so allows directional conjugation to the CLλ.

Accordingly, the present invention also provides for CLλ domainscomprising one of the following mutations: CLλ-S⁸¹K, and CLλ-K⁸⁰x/S⁸¹K,wherein x is any amino acid except P, K, R or H, wherein the numberingis according to SEQ ID NO:93. In some aspects, the invention providesfor novel CLλ domains comprising K⁸¹, or x⁸⁰/K⁸¹, wherein x is one of G,A, I, L, V, S, T, M, N, Q, F, Y, W, D, or E. In some aspects, theinvention also provides for a CLλ domain comprising a sequence selectedfrom the group consisting of SEQ ID NO:94, and SEQ ID NO:95.

Modeling also suggests that CLλ-E⁷⁷ would be available to form a saltbridge with either of CLλ-K⁸⁰ or CLλ-K⁸¹ in the same manner as CLκ-D⁷⁷appears to form a salt bridge to CLκ-K⁸⁰. Thus, mutating CLλ-E⁷⁷ to anyof R, L, S, G, Q, P, N, V, I, T, and M is likely to facilitatedirectional conjugation at either of CLλ-K⁸⁰CLλ when S⁸¹Δ (i.e. deletionof S⁸¹), or CLλ-K⁸¹. Accordingly, the present invention also providesfor a CLλ domain comprising a sequence selected from the groupconsisting of SEQ ID NO:96 and SEQ ID NO:97.

Example 40 Modeling of CLκ-K⁸⁰ Conjugation Mechanism Structure andSequence Description

Crystal structures of the Fab domain of 2.12.1.fx and h38C2-[CLκ-D⁷⁷A]were used to model the specificity of CLκ-K⁸⁰ reactivity towards ahalo-phenol (such as PFP)/ester-mediated conjugation. Experience withconjugations across multiple and varied antibodies, as well as earlymodeling analysis, indicated that modeling only needed be focused on theCLκ, as the remainder of the antibody appeared to exert very little, ifany, influence on the mechanism of conjugation.

Computational Approach

The goal of the computational calculations was to clarify the criticalattributes of CLκ-K⁸⁰ and interacting residues that preferentially biasthis site towards the PFP-ester conjugation reaction. After the 3-Dcoordinates of CLκ and CLκ-D⁷⁷A were selected from the crystal structure(based on those coordinates that contained those residues alreadyidentified as being relevant to directional conjugation), thecoordinates were subjected to standard computational protocols, such asprotein preparation, attachment of hydrogen atoms, and force fieldparameters assignment.

Hydrogen atoms were assigned to all amino acid atoms on the respective3D CLκ domain according to the calculated pKa values and pI (proteinionization potential). pKa is the value of a protonation state of agiven titratable amino acid at the neutral pH (negative logarithm ofhydrogen concentration) taking in to account the influence of aminoacids in the protein chain (Spassov; A fast and accurate computationalapproach to protein ionization. Protein Science 2008, 17, 1955-1970).The results of these calculations are shown in Table 64.

TABLE 64 pKa values of amino acid residues in CLκ Titratable residuesCalculated pKa Standard pKa CLκ-D¹⁴ 3.315 3.65 CLκ-D⁴³ 3.324 3.65CLκ-D⁵⁹ 3.667 3.65 CLκ-D⁶² 4.411 3.65 CLκ-D⁷⁷ 3.307 3.65 CLκ-E¹⁵ 3.934.25 CLκ-E³⁵ 3.906 4.25 CLκ-E⁵³ 4.604 4.25 CLκ-E⁵⁷ 4.284 4.25 CLκ-E⁷⁹3.636 4.25 CLκ-E⁸⁹ 4.244 4.25 CLκ-Y³² 10.276 10.07 CLκ-Y⁶⁵ 11.847 10.07CLκ-Y⁷⁸ 11.844 10.07 CLκ-Y⁸⁴ 14 10.07 CLκ-H⁸¹ 7.22 6.0 CLκ-H⁹⁰ 6.126 6.0CLκ-K¹⁸ 11.057 10.53 CLκ-K³⁷ 10.761 10.53 CLκ-K⁴⁰ 10.505 10.53 CLκ-K⁶¹10.852 10.53 CLκ-K⁷⁵ 10.952 10.53 CLκ-K⁸⁰ 11.119 10.53 CLκ-K⁸² 10.45110.53 CLκ-K⁹⁹ 10.706 10.53 CLκ-R³⁴ 13.428 12.48 CLκ-R¹⁰³ 14 12.48

Hydrogen atoms are added accordingly to the pKa value for all titratableamino acids and for the remaining amino acids, according to the atomicvalence number. The calculations indicated that CLκ-H⁸¹ is unprotonatedat pH 7.0-7.4 (physiological pH). This observation is consistent withproposed mechanism for catalytic reaction, where CLκ-H⁸¹ acts as anucleophilic catalyst. In general, conjugation would be expected todecrease with as the pH goes below about pH 6.5-7.0, as CLκ-H⁸¹ would beprotonated. As the pH increases above about 7.4, a greater overall levelof conjugation would be predicted, as other residues (especiallylysines) become more reactive and contribute to the overall conjugationreaction, consequently we would expect that the directional effect wouldbe increasingly lost as the pH rises. This correlates with what wasobserved in the pH study shown in Example 4, Table 4.

Minimization

CHARMm [Chemistry at HARvard Macromolecular Mechanics] is an energyminimization technique, and was used to bring the 3-D structures to theequilibrium position and find the best geometrical position for itsatomic structure. CHARMm was used at the first step with the SMARTMinimizer with 1000 steps of Steepest Descent minimization with a RMSgradient tolerance of 3[Kcal/(mol*Å)], followed by Conjugate Gradientminimization with a RMS gradient of 0.01. For the energy change, atolerance of 3[Kcal/(mol*A)] was applied to the average gradient duringa cycle of minimization. The Steepest Descent method takes the moleculeto the nearest minimum and the Conjugated Gradient improves the finalconformation obtained. Momany Rone charges were used, (as described inMomany & Rone; Validation of the general purpose QUANTA 3.2/CHARMm forcefield. Comp. Chem. 1992, 13, 888-900). The minimized structure of CLκdiffered by 1 Å when compared to the un-minimized structure.

Complex Between CLκ Domains and PFP-PEG2

The respective complexes between a PFP ester and the CLκ and CLκ-D⁷⁷Adomains was built in silico to better understand each interaction.Structural analysis of the 3D CLκ domains by the Accelrys protocolDefine and Edit Binding Site (Discovery Studio software version DS3.5)revealed a region that could be termed a ‘binding pocket’, locatedbetween the CD and EF connecting chains, and underneath CLκ-K⁸⁰, asshown in FIG. 11. This pocket is facilitated by the amino acids locatedat CLκ-K⁷⁵-E⁷⁹ (EF α-helix on the EF connecting chain), CLκ-K⁸⁰-K⁸² (EFloop on the EF connecting chain) and CLκ-V⁴² (CD loop on the CDconnecting chain) giving the shape and the electrostatic propertiesrequired by the catalytic reaction.

To measure the pocket size, the Define and Edit Binding Site protocolwas used on the previously minimized CLκ structure. This protocolrequires defining the CLκ domain as a receptor to use on it the spacefilling method to calculate the cavity size and assess its suitabilityfor binding of a molecule with a particular size, such as PFP. Thebinding site of a receptor can be represented in many ways, for examplea sphere or a list of residues surrounding this sphere. To define abinding site, the receptor is first mapped to a grid. Grid points withina given distance of the receptor atoms are marked as occupied by thereceptor, and thus undesirable as locations for ligand atoms. Twomethods exist to identify a binding site. The first uses an “eraser”algorithm to identify sites based on the shape of the receptor. Thesecond uses the volume occupied by a known ligand already positioned inan active site (Venkatachalam et al Fit: a novel method for theshape-directed rapid docking of ligands to protein active sites. J. Mol.Graph. Model 2003, 21, 289-307).

As a result of protocol execution, binding sites are identified as a setof points located on a grid that encompasses the molecule underconsideration. This definition permits measurement of the size and shapeof the binding site, which allows for its qualification as a bindingsite. PFP-PEG2 was docked manually to the site surrounded by amino acidsexperimentally identified as important for the catalytic reaction. Theseamino acids were CLκ-K⁸⁰, CLκ-H⁸¹, CLκ-D⁴³ and other amino acids within10 Å distance from CLκ-K⁸⁰ (shown in Table 54).

The initial complex between each CLκ domain and a PFP ester wasminimized using the QM/MM hybrid method, applying the CHARMm force fieldfor the CLκ domain and QM calculations for the PFP ester. The PFP esterwas minimized prior to the placement using first CHARMm then the QM/MMapproach in which the PFP ester is treated as a QM system. The structurewas minimized using the CHARMm minimization protocol described above.

For the minimizations of the complex, a QM/MM hybrid protocol was usedin which quantum mechanical (QM) calculations gave information about theelectron densities change upon interaction with WT or mutated proteinallowing us to capture the influence of the surrounding environment onthe PFP ester electron densities and its susceptibility to theconjugation reaction. The QM/MM protocol is a hybrid method where themolecular system is divided into two regions: first, the central regionPFP ester, to be treated by a QM calculation and second, the outerregion CLκ domain, treated by molecular mechanics (MM) methods.

QM treatment brings a higher level of theory, enabling the modeling ofadditional phenomena compared to traditional forcefield techniques, forexample, where a chemical reaction occurs or polarization effects playan important role. The remaining bulk of the structure is describedusing a forcefield CLκ. The way in which the two regions are allowed tointeract and how the total QM/MM energy is evaluated define the specificQM/MM protocol employed. Energy calculated in this method is composedfrom three basic parts: the QM energy of the PFP ester (E_(QM)),CD-kappa (E_(MM)), and the interaction energy between these two systems(EQ_(MMM)). The formula E_(tot)=E_(QM)+E_(MM)+E_(QM/MM) is used.

As far as the coulomb interaction between the electronic density of theQM region and the forcefield point charges is concerned, QM/MM methodsin this application always employ electronic embedding. This means thatthe forcefield atom's partial charges enter the QM calculation as anexternal potential, thereby polarizing the QM electronic densityrelative to a QM calculation in vacuo, and giving rise to anelectrostatic interaction energy between the QM density and the pointcharges. Contrary to the handling of the electrostatic interactions inQM/MM methods, the van der Waals interactions are treated entirely atthe classical level. This means that appropriate forcefield parametersmust be determined for all atoms in the simulation. The van der WaalsQM/MM interaction energy (and forces) is a part of the CHARMm simulationserver energy and is listed as a separate term in the output file.

Calculations

The total effects observed from in vitro experiments during and afterthe conjugation can be modeled by computational techniques usingstepwise approximations to describe such phenomenon as:

1. PFP binding pocket size—binding of the PFP ester and direction.

2. Protein stability—especially, the stability of a PFP binding pocket.

3. Tautomerization of the imidazole ring of CLκ-H⁸¹.

4. Directional PFP placement.

5. Initial interaction between the PFP ester and CLκ.

6. Reactivity of each of the catalytic amino acids.

Modeling Results

Identification of the binding pocket in the CLκ domain permittedmodeling and docking-placement of the PFP ester. After the PFP ester wasmodeled as docked into the respective CLκ binding site, the 3-Dstructure of the complex was minimized using a hybrid method QM/MM. Inthis approach, the PFP ester was defined as a QM system and the CLκdomain was treated by a MM method. After minimization of the complex, anetwork of intermolecular interactions between the CLκ and the PFP esterwas revealed. This network was formed by intermolecular hydrogen bonds,hydrophobic interactions, and π-electron stacking. All of these forcestogether appear to be involved in formation of a network responsible forthe directional placement and conjugation of the PFP ester to CLκ-K⁸⁰.The minimized structure of the complex indicates that CLκ-H⁸¹ is animportant catalytic amino acid.

It is known that the imidazole moiety in histidine sidechains can serveas a catalytic amino acid in enzymatic reactions, with the imidazoleacting as a nucleophile and forming an acyl imidazole during thecatalytic transition state [J Phys Chem B. 2011 Oct. 20;115(41):11895-901. Epub 2011 Sep. 23]. It is also known that theimidazole ring of histidine can undergo tautomerization, depending onwhether the Nδ or Nε atom bonds with H:

Spatial positioning of CLκ-H⁸¹ in the PFP binding pocket points to therequirement of Nδ tautomeric form of imidazole ring CLκ-H⁸¹ fornucleophilic attack on carbonyl carbon of the PFP ester. It alsoindicates a requirement for the electron lone pair at Nε to be in thesame plane as the carbonyl carbon of PFP ester group. This is possiblewhen the imidazole ring of CLκ-H⁸¹ is in the Nδ tautomeric form (seeScheme II). The tautomeric equilibrium can be controlled by the hydrogenbond interactions with the neighboring hydrogen acceptor amino acids.There are two aspartic acid residues, CLκ-D⁷⁷ and CLκ-D⁴³, in thevicinity of CLκ-H⁸¹ and both of them appear to control thetautomerization state of the CLκ-H⁸¹ imidazole ring.

FIG. 12 depicts the 3-D arrangement of CLκ-H⁸¹, CLκ-D⁴³ and CLκ-D⁷⁷,accompanied by the distances between the oxygen atoms of the asparticacids and nitrogen atoms of the imidazole ring. Hydrogen bonding betweenCLκ-D⁴³ and CLκ-H⁸¹ promote and stabilize the catalytically-activetautomeric form N6, while the hydrogen bond with CLκ-D⁷⁷ will promotethe catalytically-inactive form of CLκ-H⁸¹ Nε. In addition to thehydrogen bonds formed between CLκ-H⁸¹ Nδ and CLκ-D⁷⁷ Oδ (negativelycharged), CLκ-H⁸¹ Nε and CLκ-D⁷⁷ Oδ, CLκ-H⁸¹ Nδ can form a hydrogen bondwith the carbonyl oxygen of the CLκ-D⁷⁷ backbone. This last interactionstabilizes the catalytically-active conformation of CLκ-K⁸¹ Nδ,rendering it capable of catalysis. It is known from the mutationalanalysis and computational work discussed herein that the optimalconformation for CLκ-K⁸¹ reactivity involves hydrogen bonding withCLκ-D⁴³ via Nδ, as this stabilizes an active conformation capable of thehydrogen Hε transfer from CLκ-K⁸⁰ Nε. The two other CLκ-K⁸¹ tautomericforms will therefore most likely be less active or inactive in thecatalytic reaction.

Modeling the Effect of CLκ-D⁷⁷A Mutation

As predicted from the WT model, in the [CLκ-D⁷⁷A] domain, CLκ-H⁸¹ formsa hydrogen bond with CLκ-D⁴³ via the imidazole Nδ atom, exposingelectron pair at Nε for the nucleophilic attack on carbonyl carbon ofthe ester group in the PFP-PEG2 molecule (Scheme III). FIGS. 13A, 13Band 13C depict a comparison of crystal structure modeled CLκ andCLκ-D⁷⁷A domains, and illustrate the shift in spatial position ofCLκ-H⁸¹ in the CLκ-D⁷⁷A mutant.

Mutations to CLκ-D⁷⁷

Modeling suggests that CLκ-D⁷⁷ mutations would have a significant impacton the conjugation rate of CLκ-K⁸⁰. A series of QM/MM calculations wereconducted on the CLκ domain complexed with PFP, where CLκ-D⁷⁷ wasmutated to all other natural amino acids (CLκ-D⁷⁷C was excluded).

Modeling and experimental analysis suggests that CLκ-D⁷⁷ may bind to PFPand change the unfavorable electron density on the ester atoms of PFPmoiety involved in the catalytic reaction. The CLκ-D⁷⁷A mutation wouldthen improve the conjugation rate by allowing better distribution of theelectron densities on the reacting atoms of PFP ester.

Analysis of the calculation results performed on the mutants of CLκ-D⁷⁷indicate that the best performing mutants (in terms of conjugationefficiency) are likely to be those small hydrophobic amino acids unableto form hydrogen bonds to the PFP moiety. Modeling data thereforesuggests the mutations CLκ-D⁷⁷G, CLκ-D⁷⁷P, CLκ-D⁷⁷M, CLκ-D⁷⁷L, CLκ-D⁷⁷I, CLκ-D⁷⁷A, and CLκ-D⁷⁷V would improve directional conjugation. As seenin Example 26, this is borne out by experimental testing. All CLκ⁷⁷mutants with hydrophobic amino acids have no impact on the tautomericequilibrium of CLκ-H⁸¹, thus CLκ-H⁸¹ remains in the Nδ tautomeric formand consequently conjugation rates improve.

Modeling also suggest that most hydrophilic amino acids are likely toresult in higher protein stability than CLκ-D⁷⁷ according to by QM/MMcalculations; and points to the mutations CLκ-D⁷⁷S and CLκ-D⁷⁷T inparticular, and also CLκ-D⁷⁷Q, CLκ-D⁷⁷N, CLκ-D⁷⁷H and CLκ-D⁷⁷R aspotentially improving directional conjugation. As seen in Example 26,this is also borne out by experimental testing.

In addition to the interaction energies and the modifications of thecharge distribution, the strongest interaction and the lower conjugationrates were observed for CLκ-D⁷⁷F and CLκ-D⁷⁷Y mutants. The modelindicates that the side chains of these aromatic amino acids indtudedirectly into the binding pocket, and are likely to be involved inπ-electron stacking interactions with the PFP group and therefore changethe directional placement of PFP moiety. In addition, aromatic aminoacids can sterically hinder PFP, preventing a similar binding mode tothat possible in the WT protein thus adversely impacting the directionalplacement of the PFP moiety and resulting in a decreased conjugationrate. Interestingly, the model suggests that the side chain of CLκ-D⁷⁷Woccupies a slightly different spatial position to the aromatic sidechains of CLκ-D⁷⁷F and CLκ-D⁷⁷Y, with the CLκ-D⁷⁷W indole group sittingoutside the binding pocket and not predicted to interfere with thespatial access of a halo-phenyl ester to the binding pocket. The modelalso predicts that a conservative mutation, such as CLκ-D⁷⁷E is likelyto have a similar effect on the tautomeric form of CLκ-H⁸¹, but due tothe larger side-chain, create additional steric interference in thebinding pocket. Mutations to CLκ-D⁷⁷C or CLκ-D⁷⁷K are also predicted tointerfere with the reactivity of the site.

CLκ-D⁷⁷ favors the presence of the hydrogen atom on Nε of the imidazolering, while CLκ-D⁷⁷A favors maintaining the hydrogen at the position Nδ.Spatial distribution of amino acids in the site indicates the importantfunction Nε tautomeric form of CLκ-H⁸¹ in the catalytic reactionenabling nucleophilic attack by Nε at the carbonyl carbon of the estergroup, further facilitating directional conjugation.

Example 41 Predictive Modeling Based on Model of CLκ and CLκ-D⁷⁷A

The impact of mutations on protein stability and interaction strengthwith the PFP ester were analyzed to identify the most relevant andreactive mutants of CLκ. For this computational experiment, key aminoacids within a 10 Å distance from Cα carbon of CLκ-K⁸⁰ were selected andanalysed for (except CLκ-K⁸⁰ and CLκ-H⁸¹, given the unique requirementfor each of the residues).

For many or most of the mutations modeled for PFP conjugation with theCLκ or CLκ-D⁷⁷A, it will be understood that in certain applications, itmay appropriate to substitute or retain a residue that would reduce PFPconjugation in the CLκ or CLκ-D⁷⁷A, as it may be desirable to reduce orincrease the pocket size; such as where larger or smaller halo-phenolsare used as Z1 groups, or where the precise geometry of a specificimmunoglobulin domain appears to merit such a feature.

CLκ-K⁷⁵

This residue does not appear to have any direct impact on theconjugation reactivity of CLκ-K⁸⁰ in the native or CLκ-D⁷⁷A mutant byQM/MM calculations.

CLκ-A⁷⁶

CLκ-A⁷⁶ is located at the beginning of the α-helix, and lies and abovethe plane that contains the hydrogen-bonded carboxyl group of CLκ-D⁷⁷and the hydroxyl group of CLκ-S⁷⁴. This location allows amino acids witha large sidechain to interact with CLκ-D⁷⁷ and they may have a positiveimpact of the conjugation reaction, especially those with hydrophilicgroups capable of hydrogen bond formation. Most amino acid substitutionsat this residue would be expected to have little effect on conjugation,specifically CLκ-S⁷⁴A, CLκ-S⁷⁴D, CLκ-S⁷⁴E, CLκ-S⁷⁴1, CLκ-S⁷⁴L, CLκ-S⁷⁴M,CLκ-S⁷⁴F, CLκ-S⁷⁴W and CLκ-S⁷⁴V. Other residues that could providehydrogen bonding opportunities would be expected to enhance conjugation,namely CLκ-S⁷⁴R, CLκ-S⁷⁴N, CLκ-S⁷⁴A, CLκ-S⁷⁴H, and CLκ-S⁷⁴K, and to alesser degree CLκ-S⁷⁴S, CLκ-S⁷⁴T and CLκ-S⁷⁴Y. While residues thatdisrupt the α-helix may have a somewhat negative effect on directionalconjugation to CLκ-K⁸⁰, such as CLκ-S⁷⁴G and CLκ-S⁷⁴P, directionalconjugation is unlikely to be abrogated, merely reduced. Introduction ofa cysteine would present a risk of the potential to form aggregates inexpression.

CLκ-Y⁷⁸

CLκ-Y⁷⁸ is located on the α-helix, facing the opposite direction to thebinding pocket. CLκ-Y⁷⁸ makes a number of hydrophobic interactions withsurrounding amino acids and supports the CLκ structure. Accordingly,smaller sidechains (Ala, Ser, Thr and Val) or those that affect thestability or formation of the α-helix (Gly, Pro) will be more likely toadversely affect the conjugation reaction to CLκ-K⁸⁰, although as thesemutations are not predicted to directly interfere with the CLκ-K⁸⁰reactivity, such mutations may not necessarily abrogate directionalconjugation. Additionally, CLκ-Y⁷⁸ appear to interact with the sidechainof CLκ-R¹⁰³, thus hydrophobic or negatively-charged sidechains would beexpected to favor conjugation to facilitate this interaction (Asn, Asp,Gln, Glu, Phe and Trp). Other sidechains would not be expected to effectthe conjugation reaction (Arg, His, Ile, Leu, Lys and Met).

CLκ-E⁷⁹

Modeling suggests that the side chain of CLκ-E⁷⁹ is pointing in theopposite direction from the binding site. In addition, CLκ-E⁷⁹ appearsto form a salt bridge with sidechain of CLκ-K⁷⁵. Based on the modelling,it is postulated that most amino acid substitutions in this positionwould have little effect on the conjugation reaction (Asn, Asp, Gln,His, Met, Phe, Ser, Thr, Tyr and Trp). Small hydrophilic or chargedresidues would likely favour the conjugation reaction (Ala, Arg, Ile,Leu, Lys and Val), while those that affect the stability or formation ofthe α-helix (Gly, Pro) may adversely affect the conjugation reaction toCLκ-K⁸⁰, without necessarily abrogating directional conjugation.

CLκ-V⁸³

This residue does not appear to have a direct impact on the conjugationreaction with CLκ-K⁸⁰ by experimental data and QM/MM calculations.

TABLE 65 Summary of effect of mutations on certain CLκ residues ondirectional conjugation to CLκ-K⁸⁰. A⁷⁶ D⁷⁷ Y⁷⁸ E⁷⁹ G 0 +++ −− − P 0 +++−− − A WT ++ − + V 0 + − + L 0 ++ 0 + I 0 ++ 0 + M 0 +++ 0 0 F 0 −−− + 0W 0 + + 0 Y + −−− WT 0 T + +++ − 0 S + +++ − 0 N ++ ++ + 0 Q ++ ++ + 0 D0 WT + 0 E 0 −− + WT H ++ ++ 0 0 R ++ ++ 0 + K ++ −− 0 +

Additional Modeling CLκ-V⁴²

CLκ-V⁴² is positioned at the end of λ-strand C and the beginning of theCD loop. From a careful examination of the structure, it was observedthat CLκ-V⁴² is located underneath the imidazole ring of CLκ-H⁸¹ (FIGS.14 and 15). To help determine the nature of the interactions betweenCLκ-H⁸¹ and CLκ-V⁴², the x,y,z coordinates of the centroid for theimidazole ring were calculated, followed by measurement of the distancebetween the calculated centroid and the hydrogen atom Hδ of the CLκ-V⁴².This distance of 2.9 Å indicates direct interactions between theπ-electrons on the imidazole ring and the hydrogen Hδ of CLκ-V⁴². Thisinteraction therefore appears to strongly influence the optimalpositioning of CLκ-H⁸¹ in the pocket and for the tautomeric equilibriumshift to the Nδ tautomer. Thus, while not essential, the presence ofCLκ-V⁴² exerts a positive influence on directional conjugation. Theseanalyses are borne out by experimental data, where it was found thatCLκ-V⁴²A mutation caused a decrease in the conjugation rate (Table 54).Modeling suggests that CLκ-V⁴²I is likely to be able to assist inpositioning the CLκ-H⁸¹ imidazole ring to favour directionalconjugation, although the slightly larger side chain will reduce theoverall binding pocket size. In many circumstances, this reduction ofpocket size may not have an appreciable effect on the directionalconjugation mechanics. CLκ-V⁴²L may also be able to assist withpositioning the CLκ-H⁸¹ imidazole ring.

CLκ-D43

CLκ-D⁴³ is located on the CD loop. In native CLκ, CLκ-D⁴³ appears tointeract with the backbone of CLκ-H⁸¹ and CLκ-K⁸², contributing toprotein stability. No hydrogen bonds between Hδ of CLκ-H⁸¹ and thecarboxylic group of CLκ-D⁴³ were identified on the crystal structure ofCLκ. This may suggest that CLκ-D⁴³ exerts only a minimal influence onthe tautomeric equilibrium of the Nδ catalytically active form ofCLκ-H⁸¹. However, experimental analysis with 2.12.1.fx-[CLκ-D⁴³A]mutants showed that mutating this residue had a significant inhibitoryeffect on directional conjugation. Taken together with the overallmodel, it is likely that CLκ-H⁸¹ alternates between the catalyticallyactive and inactive form, forming H-bonds between CLκ-D⁴³ and CLκ-D⁷⁷ asit does so, and that removing the CLκ-D⁴³ residue eliminates one of theforces pushing CLκ-H⁸¹ towards the active Nδ tautomer.

Analyses of the CLκ-D⁷⁷A crystal structure revealed a well-definedhydrogen bond between hydrogen Nδ and the CLκ-D⁴³ carboxylic group. Thissuggests that one of the most significant effects of the CLκ-D⁷⁷A mutantis in stabilization of CLκ-H⁸¹ catalytically favorable tautomeric formNδ, as shown in FIGS. 13 and 14. Finally, proximity of CLκ-D⁴³ toCLκ-H⁸¹ would allow CLκ-D⁴³ to participate in the catalytic reaction asa hydrogen atom recipient in the last step of the putative reactionmechanism (Scheme III). Thus the role of CLκ-D⁴³ in the native CLκ andCLκ-D⁷⁷A mutant, appears to be in stabilization of catalytically activeNδ tautomeric form of CLκ-H⁸¹ and participation in the catalyticreaction as the hydrogen atom recipient.

The modeling analyses strongly suggests that binding of the PFP moleculein native CLκ is controlled by the tautomeric forms of CLκ-H⁸¹, and theaffinity of this binding is in turn controlled by the state of thetautomeric equilibrium constant. The presence of Nδ tautomeric formallows the lone pair on Nε to nucleophilic attack the PFP carbonyl(Scheme III).

CLκ-D⁴³ is involved in the catalytic reaction by being a hydrogen ionacceptor (Scheme III). CLκ-D⁴³ was mutated in silico to all 19 aminoacids and in the final series of calculated mutants, the WT protein(comprising CLκ-D⁴³) creates the highest interaction energy with theCLκ-PFP ester complex, with CLκ-D⁴³N also predicted to be of similarchain length and be able to form a hydrogen bond to the CLκ-H⁸¹ Nδ, thusaiding the catalytically-active tautomeric form Nδ of CLκ-H⁸¹. Otherresidues likely to be acceptable substitutions are CLκ-D⁴³E, CLκ-D⁴³Qand CLκ-D⁴³5, these being able to form the desired H-bond with CLκ-H⁸¹,but likely to have chain lengths either slightly too large or small tobe of optimal size for CLκ conjugation with PFP, but may be bettersuited to either optimizing a non-CLκ immunoglobulin domain fordirectional conjugation with PFP, or optimizing an Ig domain forconjugation with a different halo-phenyl ester.

CLκ-N⁴⁴

CLκ-N⁴⁴ is located on the CD loop. Its sidechain is pointing outwards,away from the PFP binding pocket, and appears not to have any role in,nor influence on, the conjugation reaction. QM/MM calculations predictedthat polar amino acids and those with a negatively-charged sidechain mayenhance protein stability due to the putative interactions with CLκ-K⁴¹,also located outside of the pocket.

CLκ-L⁴⁶

A CLκ-L⁴⁶A mutation had a relatively neutral impact on the conjugationrate, based on experimental data, as well as from our QM/MMcalculations. CLκ-L⁴⁶A is located outside of the PFP binding pocket, butit may facilitate the pocket shape due to the size of its sidechain.Being located outside of the pocket, it can interact with amino acidslocated outside of the pocket as well. Mutations to large andhydrophilic sidechains may increase protein stability due to theinteraction with CLκ-Q³⁹ and support the shape of the PFP pocketaccording to QM/MM calculations.

CLκ-Q⁴⁷

A CLκ-Q⁴⁷A mutation improved the conjugation rate. This mutation islikely exerting an effect by increasing the size of the PFP bindingsite, thus impacting complex formation and protein stability in apositive way according to modeling calculations. Amino acids with largersidechains will likely impact conjugation in a slightly negative way,according to QM/MM calculations. Thus, mutations to CLκ-Q⁴⁷A, CLκ-Q⁴⁷G,CLκ-Q⁴⁷V, CLκ-Q⁴⁷1, CLκ-Q⁴⁷L, CLκ-Q⁴⁷T, CLκ-Q⁴⁷S, CLκ-Q⁴⁷N, CLκ-Q⁴⁷D,CLκ-Q⁴⁷H, CLκ-Q⁴⁷P, or CLκ-Q⁴⁷E will likely be beneficial or neutral;whereas mutations to CLκ-Q⁴⁷W, CLκ-Q⁴⁷F, CLκ-Q⁴⁷Y, or CLκ-Q⁴⁷K may havea somewhat negative impact on PFP conjugation to a CLκ domain. Asbefore, it will be understood that in certain applications, it may bedesirable to reduce the pocket size; such as where smaller halo-phenolsare used as Z1 groups, or where the precise geometry of a specificimmunoglobulin domain appears to merit such a feature.

CLκ-S⁴⁸

Mutation of CLκ-S⁴⁸A improved the conjugation rates according toexperimental data: modeling suggest that the reason for this is mostlikely due to the change of electrostatic properties of the pocket.Hydrophobic amino acids at this position will therefore likely have apositive impact on the directional conjugation. Consequently, thefollowing mutations may be especially favoured: CLκ-S⁴⁸A, CLκ-S⁴⁸G,CLκ-S⁴⁸V, CLκ-S⁴⁸1, CLκ-S⁴⁸L, CLκ-S⁴⁸P, and CLκ-S⁴⁸M. Other mutationsare likely to be tolerated.

Example 42 Double and Triple Mutations of CLκ-D⁷⁷A

Antibody 2.12.1.fx was used to test the effect of further mutations tothe CLκ region. As before, numbering of residues is according to theirlocation within the CLκ (SEQ ID NO:6, for example). CLκ-D⁴³ and CLκ-H⁸¹were each mutated to Ala in on 2.12.1.fx-[CLκ-D⁷⁷A] antibody tounderstand the conjugation mechanisms. Mutations were generated on2.12.1.fx light chain following protocols described in QuickChangesite-directed mutagenesis kit (Stratagene). The antibodies 2.12.1.fx,2.12.1.fx-[CLκ-D⁷⁷A] (CLκ comprising SEQ ID NO:37), 2.12.1.fx-[CLκ-D⁴³A](CLκ comprising SEQ ID NO:15), 2.12.1.fx, 2.12.1.fx-[CLκ-D⁴³A/D⁷⁷A] (CLκcomprising SEQ ID NO:127), 2.12.1.fx-[CLκ-D⁷⁷A/H⁸¹A] (CLκ comprising SEQID NO:128), and 2.12.1.fx-[CLκ-D⁴³A/D⁷⁷A/H⁸¹A] (CLκ comprising SEQ IDNO:129), were transiently expressed in HEK 293 cells, and purified usingprotein A affinity column. The purified mAbs were characterized usingMS.

The expressed antibodies were buffer exchanged to 20 mM sodium acetate,200 mM trehalose pH 5.5 at 20 mg/ml. The antibody solutions were thenspiked with 60 mM sodium phosphate pH 7.7. [PEG₅-K¹¹-SEQ:27] (ABP) wasresuspended with 50% propylene glycol and mixed with the protein at a4.3:1 molar ratio and allowed to react overnight at room temperature.All samples were diluted to 2 mg/ml and analyzed as an intact conjugatedprotein by size exclusion chromatography-mass spectrometry (SEC-MS) todetermine the number and quantitation of conjugate forms of the protein.This technique measures the molecular weight of each protein form;multiple ABP conjugation sites are observed as distinct signalsseparated by the mass difference of an ABP. Relative quantitation ofmultiple ABP conjugation species is performed by measuring the signalmagnitude. Results of % CA are shown in Table 66.

TABLE 66 Intact conjugation analysis of 2.12.1.fx-[ CL_(K)-mutants] withABP. CL_(K) SEQ % CA ID 0 1 2 3 4 Avg CA 2.12.1.fx 6 1 15 53 26 5 2.2D⁷⁷A 37 2 3 56 32 7 2.39 D⁴³A 15 17 38 31 14 0 1.41 D⁴³A/D⁷⁷A 127 4 2146 21 7 2.06 D⁷⁷A/H⁸¹A 128 33 38 20 10 0 1.07 D⁴³A/D⁷⁷A/H⁸¹A 129 25 4028 7 0 1.18

The extent of ABP conjugation was examined separately on the light andheavy chains of 2.12.1.fx and 2.12.1.fx-[CLκ mutants]. MACs weredenatured and disulfide bonds were reduced using guanidine hydrochlorideand dithiothreitol. The resulting free light and heavy chains wereanalyzed using LCMS to determine the conjugation profile on each (Table67).

TABLE 67 Reduced heavy, light chain conjugation analysis of2.12.1.fx-[CLK- mutants]with ABP. The % of 1-LC% relative to therespective WT run is shown in the right column, as described in Table67. CLK SEQ LC % CA Avg CA- HC % CA Avg LA- ID 0 1 2 LC 0 1 HC 1LC WT %2.12.1.fx 6 23 69 8 0.85 86 14 0.14 D⁷⁷A 37 1 92 7 1.06 97 3 0.03 133D⁴³A 15 68 30 1 0.33 79 21 0.21 43 D⁴³A/D⁷⁷A 127 24 64 12 0.88 90 10 0.193 D⁷⁷A/H⁸¹A 128 72 28 0 0.28 85 15 0.15 41 D⁴³A/D⁷⁷A/H⁸¹A 129 76 20 40.28 87 13 0.13 29

These results are consistent with the His tautomer hypothesis. In theCLκ-D⁷⁷A mutant, CLκ-D⁴³ stabilizes the catalytically active tautomer ofCLκ-H⁸¹, which in turn allows CLκ-K⁸⁰ to be more receptive and reactiveto a PFP-ester. Conversely, in the CLκ-D⁴³A mutant, CLκ-D⁷⁷ stabilizesthe inactive tautomer of CLκ-H⁸¹, therefore leading to a reduction inthe directional conjugation observed at CLκ-K⁸⁰. In the double mutantCLκ-D⁴³A/D⁷⁷A, there are no interactions between CLκ-H⁸¹ and either ofCLκ-D⁴³ or CLκ-D⁷⁷, and accordingly, the double mutant acts more likethe WT CLκ.

Example 43 Rabbit CLκ Analysis

Rabbit antibody light chain kappa region (rCLκ) has the same 3Dstructure as that of other immunoglobulins. rCLκ has Asp at position 151(kabat number), Ser at position 188, and His at 189, (rCLκ-D⁴³,rCLκ-S⁸⁰, rCLκ-H⁸¹). It was postulated that a rCLκ-S⁸⁰K mutant maycreate the reaction site for PFP directional conjugation. To validatethis hypothesis, two trastuzumab rabbit chimera antibodies wereconstructed. mAb “rTrast” (rabbit trastuzumab) comprises the VL and VHdomains of trastuzumab (SEQ ID NOs:75 and 72 respectively) fused to therCLκ and rabbit constant heavy chain (rCH) (SEQ ID NOs:130 and 131respectively), to generate the full length rTrast-LC (SEQ ID NO:132) andrTrast-HC (SEQ ID NO:133).

rTrast-[rCLκ-S⁸⁰K] comprises the VL and VH domains of trastuzumab (SEQID NOs:75 and 72 respectively) fused to the rCLκ-S⁸⁰K (SEQ ID NO:134)and rabbit constant heavy chain (rCH) (SEQ ID NO:131), to generate thefull length rTrast-LC-[rCLκ-S⁸⁰K] (SEQ ID NO:135) and rTrast-HC (SEQ IDNO:133).

Rabbit IgG heavy chain and kappa1 light chain were PCRed from plasmidspFUSE-CHIg-rG and pFUSE2ss-CLIg-rk1 (Invivogen) respectively with endsoverlapping with trastuzumab variable domains and vector. Trastuzumab VHand VL were PCRed from synthetic genes with ends overlapping with vectorand rabbit constant domains. PCRs were mixed with a modified pCEP4vector (Invitrogen) cut with BglII and NheI following protocolsdescribed in Quick PCR Cloning Kit (BPS Bioscience). Insert DNA wereconfirmed by DNA sequencing. rCLκ-S⁸⁰K mutation was generated followingprotocols described in Quick PCR Cloning Kit (BPS Bioscience). Mutationwas introduced by oligonucleotide primers and cloned to a modified pCEP4vector (Invitrogen) cut with BglII and NheI. Insert DNA were confirmedby DNA sequencing.

The chimeric mAbs were transiently expressed in HEK 293 cells, andpurified using protein A affinity column. The purified mAbs werecharacterized using MS. Each of the antibodies was buffer exchanged to20 mM sodium acetate, 200 mM trehalose pH 5.5 at 20 mg/ml, and thenspiked with 60 mM sodium phosphate pH 7.7. [PEG₅-K¹¹-SEQ:27] (ABP) wasresuspended with 50% propylene glycol and mixed with the protein at a4.3:1 molar ratio and allowed to react overnight at room temperature.All samples were diluted to 2 mg/ml and analyzed as an intact conjugatedprotein by size exclusion chromatography-mass spectrometry (SEC-MS) todetermine the number and quantitation of conjugate forms of the protein.This technique measures the molecular weight of each protein form;multiple ABP conjugation sites are observed as distinct signalsseparated by the mass difference of an ABP. Relative quantitation ofmultiple ABP conjugation species is performed by measuring the signalmagnitude.

The extent of ABP conjugation was examined on the light of antibodies.MACs were denatured and disulfide bonds were reduced using guanidinehydrochloride and dithiothreitol. The resulting free light and heavychains were analyzed using LCMS to determine the conjugation profile oneach (Table 68).

TABLE 68 Intact conjugation and reduced light chain analysis of rabbitchimera conjugated with ABP. % CA Avg LC % CA Avg 1LC 0 1 2 3 CA 0 1 2CA-LC WT % rTrast 58 24 19 0 0.61 56 38 6 0.5 rTrast- 10 25 54 11 1.65718 73 8 0.89 192 [rCL_(K)-S⁸⁰K]

The rCLκ-S⁸⁰K mutation significantly increased total conjugation (0.61to 1.657) and 1CA on the light chain (38% to 73%). This result suggeststhat a directional conjugation site can be created on CLκ chains fromspecies other than human, as long as the critical residues, CLκ-K⁸⁰H⁸¹,are present on the immunoglobulin. The % of 1-LC % relative to therespective WT run is shown in the right column, as described in Table68.

Example 44 Lambda Chain

As demonstrated in Example 10 above, hCLλ does not demonstratedirectional conjugation with PFP esters. hCLλ shares sequence identitywith hCLκ at hCLκ-D⁴³ (CLλ-D⁴⁵) and hCLκ-H⁸¹ (CLλ-H⁸²), and has serinein place of hCLκ-K⁸⁰ (CLλ-S⁸¹). It was postulated that a CLλ-S⁸¹K mutantmay enable PFP conjugation to at the CLλ-S⁸¹K residue.

Comparing the crystal structures of CLκ and CLλ (FIGS. 17 & 18), CLκ-V⁴²is located at the bottom of the putative PFP binding pocket, whereas thecorresponding residue in CLλ is CLλ-A⁴⁴. As discussed above, CLκ-V⁴²Amutations have a negative impact on the directional conjugation, likelyowing to the ability of CLκ-V⁴² to stabilize the orientation of theimidazole ring of CLκ-H⁸¹. Modeling suggested that a CLλ-A⁴⁴V mutationshould exert a similar effect on CLλ-H⁸².

As in Example 10, and Examples 15-17, a monoclonal anti-human IL22antibody (hIL22) was used as an exemplary CLλ comprising antibody. hIL22comprised SEQ ID NOs:136 and 137 (hIL22-LC and hIL22-HC respectively),and variable light chain comprising SEQ ID NO:138 (hIL22-CLλ-VL).

A number of mutant versions of hIL22 were generated, to assess theeffects of various CLλ mutations on directional conjugation. All hIL22mutant antibodies comprised SEQ ID NO:137 (hIL22-HC), and SEQ ID NO:138(hIL22-CLλ-VL).

hIL22-[LKJ] comprised the λ/κ swap as described in Example 15, andcomprised a CL of SEQ ID NO:61. hIL22-[CLλ-S⁸¹K] comprised the singleresidue swap of CLλ-S⁸¹K, and comprised SEQ ID NO:140.hIL22-[CLλ-Q⁷⁸A/S⁸¹K] comprised a double mutation in the loop, andcomprised SEQ ID NO:141. hIL22-[CLλ-A⁴⁴V/S⁸¹K] comprised the CLλ-S⁸¹Kresidue swap, and also a CLλ-A⁴⁴V mutation at the bottom of the “bindingpocket”, and comprised SEQ ID NO:142. hIL22-[CLλ—A⁴⁴V/Q⁷⁸A/S⁸¹K]comprised both loop mutations CLλ-Q⁷⁸A and CLλ-S⁸¹K, as well as the“binding pocket” CLλ-A⁴⁴V mutation, and comprised SEQ ID NO:143. All thepoint mutations were generated on hIL22-LC following protocols describedin QuickChange site-directed mutagenesis kit (Stratagene). Mutationswere introduced by oligonucleotide primers and confirmed by DNAsequencing.

hIL22-[CLλ-A⁷⁶⁻⁸⁴/145] comprised inserting SEQ ID NO:145 in place of theCLλ E-F loop, located from CLλ-P⁷⁶ inclusive through to CLλ-S⁸³inclusive. SEQ ID NO:145 comprises the sequence KAAYEKHKV, whichcorresponds to the [CLκ-D⁷⁷A] E-F loop (i.e. between β-strands E and F)from [CLκ-D⁷⁷A]-K⁷⁵ inclusive through to [CLκ-D⁷⁷A]-K⁸² inclusive.

hIL22-[CLλ-A⁷⁶⁻⁸⁴/145] was generated by overlap PCR. Mutations wereintroduced by oligonucleotide primers. Primer specific to the 5′ end ofhIL22-LC paired with a reverse primer encoding SEQ ID NO:145, and aforward primer encoding SEQ ID NO:145, paired with the reverse primerspecific to the 3′ end of IL22-LC were used to PCR amplify DNA fragmentscarrying CLκ E-F loop using IL22-LC as template. These two PCR productswere mixed as templates; IL22-LC forward primer and reverse primer wereused in overlap PCR reaction to amplify the full length IL22-LC DNA withSEQ ID NO:145. The PCR was then digested with restriction enzyme BglIIand NheI. The digested PCR was ligated with a modified pCEP4 plasmid(Invitrogen) cut with BglII and NheI.

The mutated mAbs were transiently expressed in HEK 293 cells, andpurified using protein A affinity column. The purified mAbs werecharacterized using MS.

Each of the antibodies was buffer exchanged to 20 mM sodium acetate, 200mM trehalose pH 5.5 at 20 mg/ml, and then spiked with 60 mM sodiumphosphate pH 7.7. [PEG₅-K¹¹-SEQ:27] (ABP) was resuspended with 50%propylene glycol and mixed with the protein at a 4.3:1 molar ratio andallowed to react overnight at room temperature. All samples were dilutedto 2 mg/ml and the extent of ABP conjugation was examined separately onthe light and heavy chains of antibodies. The MACs were denatured anddisulfide bonds were reduced using guanidine hydrochloride anddithiothreitol. The resulting free light and heavy chains were analyzedusing LCMS to determine the conjugation profile on each (Table 69).

TABLE 69 Reduced heavy, light chain conjugation analysis of lambdaantibody and mutants. CL LC % CA HC % CA Ab conjugated SEQ Ave Ave withABP ID 0 1 2 LC 0 1 2 HC 2.12.1.fx 6 15 79 6 0.91 93 7 0 0.072.12.1.fx-CL_(K)-D⁷⁷A 37 0 92 8 1.08 98 2 0 0.02 Trastuzumab-WT 76 32 662 0.7 83 17 0 0.17 Trastuzumab- 77 0 95 5 1.05 90 10 0 0.1 CL_(K)-D⁷⁷AhIL22 136 100 0 0 0 76 22 2 0.26 hIL22-[LKJ] 61 55 45 0 0.45 79 21 00.21 hIL22-[CLλ-S⁸¹K] 140 69 31 0 0.31 80 20 0 0.2 hIL22- 141 89 11 00.11 85 15 0 0.15 [CLλ-Q⁷⁸A/S⁸¹K] hIL22- 142 48 52 0 0.52 87 13 0 0.13[CLλ-A⁴⁴V/S⁸¹K] hIL22- [CLλ-A⁴⁴V/ 143 30 70 0 0.7 82 18 0 0.18Q⁷⁸A/S⁸¹K] hIL22- 144 83 17 0 0.34 82 18 0 0.2 [CLλ-λ⁷⁶⁻⁸⁴/145]

A single point mutation CLλ-S⁸¹K enabled PFP conjugation to the CLλ. TheLC % 1CA increased from 0% to 31% on the CLλ-S⁸¹K mutant comparedagainst the unmutated hIL22, with more conjugation additions seeminglyoccurring at the newly created conjugation site than at any other singlesite on the antibody. Peptide mapping studies confirmed that theconjugation events were occurring on CLλ-S⁸¹K (Table 70).

TABLE 70 Overview of peptide mapping studies on hIL22-[CLλ-S⁸¹K]-CL.Average Δ (% conjugation, Protein Chain Peptide n = 3)hIL22-[CLλ-S⁸¹K]-CL SEQ ID NO: 140, residues 80-85  54 ± 10hIL22-[CLλ-S⁸¹K]-HC SEQ ID NO: 137, residues 96-103 21 ± 10hIL22-[CLλ-S⁸¹K]-HC SEQ ID NO: 137, residues 95-103 19 ± 10

Referring back to Table 69, combining mutations at CLλ-S⁸¹K and CLλ-A⁴⁴V(hIL22-[CLλ-A⁴⁴V/S⁸¹K]) further increased light chain 1CA to 52%.

Interestingly, while the CLλ-Q⁷⁸A/ CLλ-S⁸¹K double mutation did improveconjugation of the CLλ-S⁸¹K compared to WT CLλ (1 CA from 0% to 11%),the improvement was less pronounced than that seen in the singleCLλ-S⁸¹K mutant. This correlates well with the model: the effect ofmutating CLκ-D⁷⁷ is to remove the hydrogen bond between CLκ-D⁷⁷ andCLκ-H⁸¹, enabling CLκ-H⁸¹ to revert to the catalytically tautomeric Nδform. The corresponding position to CLκ-D⁷⁷ is CLλ-Q⁷⁸, which bothmodeling and mutational analysis suggest would not have a limitingeffect on CLλ-H⁸². Taken together, this suggests that the diminishingeffect of CLλ-Q⁷⁸A on the directional conjugation is likely caused by analteration to the size and shape of the binding pocket.

Most surprising, however, was the result of the triple mutationCLλ-A⁴⁴V/Q⁷⁸A/S⁸¹K. Directional conjugation as measured by the 1CA %increased to 70%; reaching levels typically seen in native CLκ domains.

These results and analysis were borne out by the similar level ofdirectional conjugation seen in the loop swap (hIL22-[CLλ-A⁷⁶⁻⁸⁴/145]).

Overall, these data suggested that the CLλ-Q⁷⁸A mutation does improvedirectionality of CLλ-S⁸¹K conjugation, provided the size and shape ofthe binding pocket is adapted for the specific Z group used. Moreover,the results of CLλ mutants suggested that directional conjugation sitescan be created on immunoglobulins other than CLκ, provided that themotif KH is present in the correct 3D location. Naturally, the bindingpocket must be of suitable size and shape to accommodate the specifichalo-phenyl ester employed, and, as demonstrated herein, additionalfeatures, such as the presence or absence of residues corresponding toCLκ-V⁴², CLκ-D⁴³, and CLκ-D⁷⁷ can have significant effects on the rateand optimization of directional conjugation of the KH motif relative tothe specific immunoglobulin domain and halo-phenyl ester. While PFP wasused in these examples, it will be apparent that other Z groups withacceptable levels of directional conjugation may be selected, and usingrational modeling techniques, a balance may be obtained between thedesired Z group, size of the binding pocket and the specific mutationsrequired to maintain an active binding pocket.

Example 45 Recreating PFP Conjugation Sites on CH Domains

The CH domains of antibodies also comprise immunoglobulin structures.Prior to modeling the domains as described in Examples 40 and 41, it waspostulated that moving the conjugation motif to the EF loop portion ofthe EF connecting chain of other CH domains may permit directionalconjugation. A sequence alignment of the CHγ1 (SEQ ID NO:147), CHγ2 (SEQID NO:155), CHγ3 (SEQ ID NO:158), CLκ (SEQ ID NO:6) and CLλ (SEQ IDNO:57) domains is shown in FIG. 16.

Two mutant versions were made on the CH1 domain.

In hCHγ1-m1, the sequence LGTQT (SEQ ID NO:152), which corresponds toresidues L⁷⁶-T⁸⁰ of SEQ ID NO:147, was removed, and replaced by EKHKV(SEQ ID NO:153), which corresponds to E⁷⁹-V⁸³ of CLκ. The resultantmutant, hCHγ1-m1, comprised SEQ ID NO:148.

In CHγ1-m2, the sequence LGTQT (SEQ ID NO:152), which corresponds toresidues L⁷⁶-T⁸⁰ of SEQ ID NO:147, was removed, and replaced by YEKHKV(SEQ ID NO:154), which corresponds to Y⁷⁸-V⁸³ of CLκ-. The resultantmutant, hCHγ1-m2, comprised SEQ ID NO:150. The additional Y residue wasincorporated to allow the hCHγ1-m2 sequence to better align with CLκsequence.

Sequence alignment indicated that hCHγ1 lacks an Asp residuecorresponding to CLκ-D⁴³. Accordingly, two additional mutants weregenerated; where each of hCHγ1-m1 and hCHγ1-m2 were subjected to anadditional insertional mutation of an Asp residue between CHγ1-S⁴³ andCHγ1-G⁴⁴, creating the two new mutants of hCHγ1-m1-D44 (SEQ ID NO:149)and hCHγ1-m2-D⁴⁴ (SEQ ID NO:151).

A mutant version of hCHγ2 (SEQ ID NO:155) was generated, where residuesN⁸⁵G⁸⁶ or SEQ ID NO:155 were substituted with KH to generate hCHγ2-m(SEQ ID NO:156). Sequence alignment suggested that hCHγ2 (SEQ ID NO:155)comprised an Asp residue (D⁵⁰) at a location that may correspond toCLκ-D⁴³.

A mutant version of hCHγ3 (SEQ ID NO:157) was generated, where residuesQ⁷⁹G⁸⁰ of SEQ ID NO:157 were substituted with KH to generate hCHγ3-m(SEQ ID NO:158). Sequence alignment suggested that hCHγ3 (SEQ ID NO:155)comprised an Asn residue (N⁴⁴) at a location corresponding to CLκ-D⁴³.

Trastuzumab was used as a model Ab in the study. All the hTrast-CHγmutants were expressed with a [CLκ-K⁸⁰A] mutation, so that conjugationevents would preferentially occur on the test CHγ domain. ThehTrast-LC-[CLκ-K⁸⁰A] (SEQ ID NO:146) mutation was generated followingprotocols described in QuickChange site-directed mutagenesis kit(Stratagene).

The mutations on CHγ domains were generated using overlap PCR. Mutationswere introduced by oligonucleotide primers. Primer specific to the 5′end of trastuzumab HC paired with a reverse primer carrying the desiredmutation, and a forward primer carrying the desired mutation paired withthe reverse primer specific to the 3′ end of trastuzumab HC were used toPCR amplify DNA fragments using trastuzumab HC as template. These twoPCR products were mixed as templates; trastuzumab heavy chain forwardprimer and reverse primer were used in overlap PCR reaction to amplifythe full length trastuzumab HC DNA with desired mutations. The PCR wasthen digested with restriction enzyme BglII and NheI. The digested PCRwas ligated with a modified pCEP4 plasmid (Invitrogen) cut with BglIIand NheI.

The trastuzumab antibody carrying mutations were transiently expressedin HEK 293 cells, and purified using protein A affinity column. Thepurified mAbs were characterized using MS.

The expressed antibody was buffer exchanged to 20 mM sodium acetate, 200mM trehalose pH 5.5 at 20 mg/ml. The proteins were then spiked with 60mM sodium phosphate pH 7.7. ABP was resuspended with 50% propyleneglycol and mixed with the protein at a 4.3:1 molar ratio and allowed toreact overnight at room temperature. All samples were diluted to 2 mg/mland analyzed as an intact conjugated protein by size exclusionchromatography-mass spectrometry (SEC-MS) to determine the number andquantitation of conjugate forms of the protein. This technique measuresthe molecular weight of each protein form; multiple ABP conjugationsites are observed as distinct signals separated by the mass differenceof an ABP. Relative quantitation of multiple ABP conjugation species isperformed by measuring the signal magnitude.

TABLE 71 Intact conjugation analysis of hTrast antibody and CHγ domainmutants. % CA Ab + ABP 0 1 2 3 Avg CA hTrast 1 16 56 24 2.112hTrast-[CLκ-D77A] 0 1 62 34 2.338 hTrast-[CLκ-K80A] 48 41 10 2 0.665hTrast-[CLκ-K⁸⁰A]/CHγ1-m1 23 48 24 5 1.107 hTrast-[CLκ-K⁸⁰A]/CHγ1-m2 2448 24 4 1.087 hTrast-[CLκ-K⁸⁰A]/CHγ1-m1-D⁴⁴ 33 49 17 1 0.854hTrast-[CLκ-K⁸⁰A]/CHγ1-m2-D⁴⁴ 41 45 12 2 0.746 hTrast-[CLκ-K⁸⁰A]/CHγ2m45 44 9 3 0.694 hTrast-[CLκ-K⁸⁰A]/CHγ3m 40 44 13 3 0.78

The extent of ABP conjugation was examined separately on the light andheavy chains of trastuzumab and trastuzumab mutants. MAC product wasdenatured and disulfide bonds were reduced using guanidine hydrochlorideand dithiothreitol. The resulting free light and heavy chains wereanalyzed using LCMS to determine the conjugation profile on each chain(Table 72).

TABLE 72 Reduced heavy, light chain conjugation analysis of hTrastantibody and CHy domain mutants. The % of 1-HC % relative to therespective WT run is shown in the right column, as described in Table53, although in this example, hTrast-[CLK-K⁸⁰A]HC 1CA was taken as theWT figure. LC % CA HC % CA Avg Avg CA- CA- 1HC 0 1 2 LC 0 1 2 HC WT %hTrast 32 66 2 0.7 83 17 0 0.17 N/A hTrast-[CL_(K)-D⁷⁷A] 0 95 5 1.05 9010 0 0.1 N/A hTrast-[CL_(K)-K⁸⁰A] 98 2 0 0.02 79 21 0 0.21hTrast-[CL_(K)-K⁸⁰A]/CHγ1-m1 99 1 0 0.01 64 31 5 0.41 148hTrast-[CL_(K)-K⁸⁰A]/CHγ1-m2 98 2 0 0.02 62 32 6 0.44 152hTrast-[CL_(K)-K⁸⁰A]/CHγ1-m1-D⁴⁴ 97 3 0 0.03 74 24 2 0.28 114hTrast-[CL_(K)-K⁸⁰A]/CHγ1-m2-D⁴⁴ 97 3 0 0.03 73 24 3 0.3 114hTrast-[CL_(K)-K⁸⁰A]/CHγ2m 99 1 0 0.01 75 23 2 0.27 110hTrast-[CL_(K)-K⁸⁰A]/CHγ3m 100 0 0 0 70 27 3 0.33 129

The total conjugation on hTrast-[CLκ-K⁸⁰A]/CHγ1-m1 andhTrast-[CLκ-K⁸⁰A]/CHγ1-m2 were increased compared to hTrast-[CLκ-K⁸⁰A],from 0.66 CA to ˜1 CA; and the HC 1 CA of these two mutants increasedfrom 21% to 31%, and improvement of about 150% This supports thehypothesis that directional conjugation can be introduced toimmunoglobulin domains other than CLκ and CLλ by the introduction of theKH motif.

The total conjugation on hTrast-[CLκ-K⁸⁰A]/CHγ2m also increased, but toa lesser extent than that of the CHγ1 mutants. A comparison of thesequences of the CHγ1 and CHγ2 sequences shows that at the residuecorresponding to CLκ-D⁷⁷, CHγ1 comprises Ser, and CHγ2 comprises Asp.This could suggest that a mutation similar to the CLκ-D⁷⁷ mutations inCHγ2 domains could improve the extent of conjugation.

In addition, the improvement in conjugation on the CHγ3 HC, whileevident, was also modest in comparison to the CHγ1 domain mutants. TheCHγ3 domain sequence appeared to comprise Arg at a positioncorresponding to CLκ-D77, and Ser at a position corresponding toCLκ-D⁴³.

Furthermore, the conjugation of the CA % HC for bothhTrast-[CLκ-K⁸⁰A]/CHγ1-m1-D⁴⁴ and hTrast-[CLκ-K⁸⁰A]/CHγ1-m2-D⁴⁴ showed avery surprising result, in that the apparent increase in conjugationseen in both hTrast-[CLκ-K⁸⁰A]/CHγ1-m1 and hTrast-[CLκ-K⁸⁰A]/CHγ1-m2went from approximately 150% of WT to only about 114% of WT.

An explanatory hypothesis suggested that the sequence alignment of FIG.17 may not accurately align the respective residues according to wherethey are found on a 3D immunoglobulin structure.

Example 46 Modeling the Immunoglobulin Fold

Consequently, crystal structure coordinates for the hCHγ1, hCHγ2 andhCHγ3 domains were obtained from the “Protein Data Bank”, maintained byRutgers, the State University of New Jersey, Center for IntegrativeProteomics Research, the San Diego Supercomputer Center (SDSC) andSkaggs School of Pharmacy and Pharmaceutical Sciences, San Diego. Thestructure of hCHλ1 is based on X-ray structure of 3dv, available throughthe “Protein Data Bank”. The structure of hCHλ2 is based on the X-raystructure of 2dts available through the “Protein Data Bank”. Thestructure of hCHλ3 is based on the X-ray structure of 2dts availablethrough the “Protein Data Bank”. The structure of hCLλ is based on theX-ray structure of 4fqh available through the “Protein Data Bank”.

An homology alignment was generated, which aligned the sequencesaccording to structure (FIG. 17). Crystal structure comparisons of CLκand hCHγ1-m1 (FIG. 19) showed that the hCHγ-CD connecting chaincomprised a short α-helix. Modeling suggested that this CD α-helixpresents the native S⁴³ and the hTrast-[CLκ-K⁸⁰A]/CHγ1-ml-D44 Aspinsertion with side chains extending away from the binding pocket (FIGS.20 & 21), and that the addition of CHγ1-D⁴⁴ increases the size of andextends the CD α-helix. In addition, the model suggests that theCHγ1-Q⁷⁹H residue is not in the optimal planar orientation, reducing itsability to participate in the reaction between PFP and the adjacentCHγ1-T⁷⁸K (FIG. 21).

A comparison of the CLκ and CHγ1-m1-D44 domains of FIG. 22 suggests thatthe pocket shape may be optimized by removing the CD α-helix on the CDconnecting chain, and replacing with a loop structure. Accordingly, amutant CHγ1 domain, SEQ ID NO:165, was modelled and minimized. SEQ IDNO:165 comprises the CHγ1-T⁸⁴K/Q⁷⁹H double mutation of the CHγ1-m1mutant, as well as substituting the CHγ1 CD connecting chain fromCHγ1-N⁴² inclusive through to CHγ1-L⁴⁶ inclusive with KVDNALA (SEQ IDNO:166); SEQ ID NO:166 corresponds to residues of the CLκ domain (SEQ IDNO:6), with an additional Ala residue added. Modeling results shown inFIG. 22 suggest that CHγ1-Q⁷⁹H occupies a more planar orientation,assisted by the introduced Val residue on the CD connecting chain.Mutating this residue to Leu or Ile may provide further stabilization tothe imidazole ring, owing to the longer side chains being able to closethe increased gap to the H residue, relative to the distance in nativeCLκ. Significantly, the model places the adjacent Asp residue in asuitable orientation and distance from CHγ1-Q⁷⁹H to favour the6-tautomeric form, and promote increased reactivity of CHγ1-T⁷⁸K.

Similar modeling was performed on the CHγ2 and CHγ3 domains. FIG. 24compares key WT residues of CLκ and CHγ2. While CHγ2-D⁴⁹ and CHγ2-D⁵⁰appear to be in the correct position and orientation to assist withdirectional conjugation, CHγ2-D⁸² occupies a position even closer toCHγ2-G⁸⁶H in the 3D model, thereby favouring the ε-tautomeric form, andreducing the reactivity of CHγ2-N⁸⁵K. This model suggests that theCHγ2-D⁸² residue may explain the relatively low increase in directionalconjugation seen in the CHγ2m mutant. FIG. 26 illustrates a minimizedmodel of a proposed mutant for CHγ2: comprising the mutationsCHγ2-D⁸²A/N⁸⁵K/G⁸⁶H (SEQ ID NO:167). An immediate difference is seen:the imidazole ring appears in a more planar orientation, and within asuitable distance to CHγ2-D⁵⁰ to bias formation of the δ-tautomer, andthe CHγ2-D⁸²A mutation has opened up the binding pocket, likely leadingto a reduction in steric inhibition of PFP access.

FIGS. 27-29 show the corresponding comparisons of CLκ with CHγ3 WT, andCHγ3m mutant. The model suggests that despite there being no residuebiasing CHγ3-G⁸⁰H towards the ε-tautomer form, the availability ofCHγ3-Q⁷⁹K to conjugate is likely sterically hindered by the longCHγ3-R⁷⁶ side-chain. FIG. 30 illustrates a minimized model of a firstproposed mutant for CHγ3: hCH3γm-CD1/EF, comprising the mutationsCHγ3-S⁴³V/N⁴⁴D/R⁷⁶A/Q⁷⁹K/G⁸⁰H (SEQ ID NO:168). The modeled differencecan be easily observed in FIG. 30B: the availability of the bindingpocket has opened up, and reduced steric interference on the reactiveLys.

From the sidechain distances in the modeled structure of FIG. 30B, it isunlikely that CHγ3-S⁴³V or CHγ3-N⁴⁴D interact with CHγ3-G⁸⁰H to the sameextent as the corresponding residues in CLκ. Accordingly, a secondproposed mutant for CHγ3 was also minimized and modeled: hCH3γm-CD2/EF,comprising the mutations CHγ3-S⁴³L/N⁴⁴E/R⁷⁶A/Q⁷⁹K/G⁸⁰H (SEQ ID NO:169).The introduction of suitable residues on the CD connecting chain withlonger side chains (CHγ3-S⁴1 instead of CHγ3-S⁴³V, and CHγ3-N⁴⁴E insteadof CHγ3-E⁴⁴D) is modeled to have a binding pocket with greater structuresimilarities to that of CLκ (FIG. 31), and a greater likelihood ofhydrogen bonding between CHγ3- N⁴⁴E and CHγ3-G⁸⁰H than between CHγ3-N⁴⁴D and CHγ3-G⁸⁰H.

Sequences of the CHγ domains and mutants were aligned with the CLκ andCLλ (FIG. 32).

The invention thus has been disclosed broadly and illustrated inreference to representative embodiments described above. Those skilledin the art will recognize that various modifications can be made to thepresent invention without departing from the spirit and scope thereof.All publications, patent applications, and issued patents, are hereinincorporated by reference to the same extent as if each individualpublication, patent application or issued patent were specifically andindividually indicated to be incorporated by reference in its entirety.Definitions that are contained in text incorporated by reference areexcluded to the extent that they contradict definitions in thisdisclosure.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable sub-combination.

It is specifically contemplated that any limitation discussed withrespect to one embodiment of the invention may apply to any otherembodiment of the invention. Furthermore, any composition of theinvention may be used in any method of the invention, and any method ofthe invention may be used to produce or to utilize any composition ofthe invention. In particular, any aspect of the invention described inthe claims, alone or in combination with one or more additional claimsand/or aspects of the description, is to be understood as beingcombinable with other aspects of the invention set out elsewhere in theclaims and/or description and/or sequence listings and/or drawings

In so far as specific examples found herein do not fall within the scopeof an invention, said specific example may be explicitly disclaimed.

The use of the term “or” in the claims is used to mean “and/or” unlessexplicitly indicated to refer to alternatives only or the alternativeare mutually exclusive, although the disclosure supports a definitionthat refers to only alternatives and “and/or.” As used herein thespecification, “a” or “an” may mean one or more, unless clearlyindicated otherwise. As used herein in the claim(s), when used inconjunction with the word “comprising”, the words “a” or “an” may meanone or more than one. As used herein “another” may mean at least asecond or more. Unless otherwise defined herein, scientific andtechnical terms used in connection with the present invention shall havethe meanings that are commonly understood by those of ordinary skill inthe art. Further, unless otherwise required by context, singular termsshall include pluralities and plural terms shall include the singular.The words “comprises/comprising” and the words “having/including” whenused herein with reference to the present invention are used to specifythe presence of stated features, integers, steps or components but doesnot preclude the presence or addition of one or more other features,integers, steps, components or groups thereof.

TABLE 73 Toxin # IUPAC name STRUCTURE #542-Methylalanyl-N-[(3R,4S,5S)-3- methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-2-methyl-3-oxo-3-{[(1S)- 2-phenyl-1-(1,3-thiazol-2-yl)ethyl]amino}propyl]pyrrolidin-1- yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide (#54

#226 N,2-dimethylalanyl-N-[(3R,4S,5S)-3- methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-3-{[(2S)-1-methoxy-1- oxo-3-phenylpropan-2-yl]amino}-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide (#226)

#194 N,2-{[(3S)-3-fluoropyrrolidin-3- yl]carbonyl}-N-[(3R,4S,5S)-3-methoxy-1-{(2S)-2-[(1R,2R)-1- methoxy-2-methyl-3-oxo-3-{[(1S)-2-phenyl-1-(1,3-thiazol-2- yl)ethyl]amino}propyl]pyrrolidin-1-yl}-5-methyl-1-oxoheptan-4-yl]-N- methyl-L-valinamide, trifluoroaceticacid salt (#194)

#192 N,2-{[(3R)-3-fluoropyrrolidin-3- yl]carbonyl}-N-[(3R,4S,5S)-3-methoxy-1-{(2S)-2-[(1R,2R)-1- methoxy-2-methyl-3-oxo-3-{[(1S)-2-phenyl-1-(1,3-thiazol-2- yl)ethyl]amino}propyl]pyrrolidin-1-yl}-5-methyl-1-oxoheptan-4-yl]-N- methyl-L-valinamide, trifluoroaceticacid salt (#192)

#201 1,2-dimethyl-D-proly-N- [(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(2S)-3-(4-aminophenyl)-1- methoxy-1-oxopropan-2-yl]amino}-1-methoxy-2-methyl-3- oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4- yl]-N-methyl-L-valinamide, formate salt(#201)

#158 N-{(2R,3R)-3-methoxy-3-[(2S)-1- {(3R,4S,5S)-3-methoxy-5-methyl-4-[methyl(N-{[(2S)-2- methylpiperidin-2-yl]carbonyl}-L-valyl)amino]heptanoyl}pyrrolidin- 2-yl]-2-methylpropanoyl}-L-phenylalaninate, trifluoroacetic acid salt (#158)

#70 2-methylalanyl-N-[(3R,4S,5S)-3- methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-3-{[(2S)-1-methoxy-1- oxo-3-phenylpropan-2-yl]amino}-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide (#70)

#47 N²-[(1-Aminocyclopentyl)carbonyl]-N-[(3R,4S,5S)-3-methoxy-1-{(2S)-2- [(1R,2R)-1-methoxy-2-methyl-3-oxo-3-{[(1S)-2-phenyl-1-(1,3- thiazol-2-yl)ethyl]amino}propyl]pyrrolidin-1- yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide (#47)

#130 N,2-dimethylalanyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(2S)-1-tert- butoxy-1-oxo-3-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3- oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4- yl]-N-methyl-L-valinamide (#130)

#159 methyl N-{(2R,3R)-3-methoxy-3- [(2S)-1-{(3R,4S,5S)-3-methoxy-5-methyl-4-[methyl(N-{[(2R)-2- methylpiperidin-2-yl]carbonyl}-L-valyl)amino]heptanoyl}pyrrolidin- 2-yl]-2-methylpropanoyl}-L-phenylalaninate, trifluoroacetic acid salt (#159)

#209 1,2-dimethyl-L-proly-N-[(3R,4S,5S)- 3-methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-3-{[(2S)-1-methoxy-1- oxo-3-phenylpropan-2-yl]amino}-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide, trifluoroacetic acid salt (#209)

#131 2-methyl-D-prolyl-N-[(3R,4S,5S)-3- methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-3-{[(2S)-1-methoxy-1- oxo-3-phenylpropan-2-yl]amino}-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide, trifluoroacetic acid salt (#131)

#117 2-methyl-L-prolyl-N-[(3R,4S,5S)-3- methoxy-1-{(2S)-2-[(1R,2R)-1-methoxy-3-{[(2S)-1-methoxy-1- oxo-3-phenylpropan-2-yl]amino}-2- methyl-3oxopropyl]pyrrolidin-1- yl}-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide, trifluoroacetic acid salt (#117)

#115 N,2-dimethylalanyl-N-{(1S,2R)-4-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy- 2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-2-methoxy-1-[(1S)-1-methylpropyl]-4-oxobutyl}-N- methyl-L-valinamide, trifluoroacetic acidsalt (115)

#69 2-Methylalanyl-N-[(3R,4S,5S)-1- {(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-1-methoxy- 2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1- oxoheptan-4-yl]-N-methyl-L- valinamide (#69)

#151 1,2-dimethyl-L-prolyl-N-{(1S,2R)-4-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy- 2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-2-methoxy-1-[(1S)-1-methylpropyl]-4-oxobutyl}-N- methyl-L-valinamide (#151)

#162 N-{(2R,3R)-3-methoxy-3-[(2S)-1- {(3R,4S,5S)-3-methoxy-5-methyl-4-[methyl(N-{[(2S)-2- methylpiperidin-2-yl]carbonyl}-L-valyl)amino]heptanoyl}pyrrolidin- 2-yl]-2-methylpropanoyl}-L-phenylalanine, trifluoroacetic acid salt (#162)

#153 1,2-dimethyl-D-prolyl-N-{(1S,2R)-4-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy- 2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-2-methoxy-1-[(1S)-1-methylpropyl]-4-oxobutyl}-N- methyl-L-valinamide (#153)

#118 2-methyl-L-prolyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy- 2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1- yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L- valinamide, trifluoroacetic acid salt (#118)

#163 N-{(2R,3R)-3-methoxy-3-[(2S)-1- {(3R,4S,5S)-3-methoxy-5-methyl-4-[methyl(N-{[(2R)-2- methylpiperidin-2-yl]carbonyl}-L-valyl)amino]heptanoyl}pyrrolidin- 2-yl]-2-methylpropanoyl}-L-phenylalanine, trifluoroacetic acid salt. (#163)

#217 N-{(2R,3R)-3-[(2S)-1-{(3R,4S,5S)-4-[(N-{[(3R)-3-fluoropyrrolidin-3- yl]carbonyl}-L-valyl)(methyl)amino]-3-methoxy-5- methylheptanoyl}pyrrolidin-2-yl]-3-methoxy-2-methylpropanoyl}-L- phenylalanine, trifluoroacetic acid salt(#217)

#112 2-methylalanyl-N-[(3R,4S,5S)-1- {(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2- yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3- methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide (#112)

MMAD The wavy line indicates a typical location for linker attachment.In non-conjugated form, the wavy line is typically conneted to a H atom.

MMAE The wavy line indicates a typical location for linker attachment.In non-conjugated form, the wavy line is typically conneted to a H atom.

MMAF The wavy line indicates a typical location for linker attachment.In non-conjugated form, the wavy line is typically connected to a Hatom.

1. A polypeptide comprising an immunoglobulin domain comprising 7β-strands A, B, C, D, E, F, and G sequentially connected together bychains of connecting amino acids, wherein the β-strands are arranged soas to form a first β-sheet comprising β-strands A, B, D, and E, and asecond β-sheet comprising β-strands C, F and G, said first and secondβ-sheets being covalently bonded together; wherein β-strands E and F areconnected together by an EF chain, and said EF chain comprises thesequence, X¹-X²-X³-X⁴-K⁵⁻H⁶ (SEQ ID NO:98), and wherein X¹, X³ and X⁴are each independently any amino acid residue, and characterized in thatX² is selected from the group consisting of A, G, I, V, L, R, S, T, Q,P, N, M, H, W, and pharmaceutically acceptable salts, stereoisomers,tautomers, solvates, and prodrugs thereof.
 2. The polypeptide as claimedin claim 1, wherein the EF chain comprises a sequence selected from thegroup consisting of SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:101, SEQ IDNO:102, SEQ ID NO:103, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:117, SEQID NO:118, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:125, SEQ ID NO:126,SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:173, SEQ IDNO:174, SEQ ID NO:175, SEQ ID NO:176, SEQ ID NO:177, SEQ ID NO:178, SEQID NO:179, SEQ ID NO:180, SEQ ID NO:181, SEQ ID NO:182, SEQ ID NO:183,SEQ ID NO:184, SEQ ID NO:185, SEQ ID NO:186, SEQ ID NO:187, SEQ IDNO:188, SEQ ID NO:189, SEQ ID NO:190, SEQ ID NO:191, SEQ ID NO:192, SEQID NO:193, SEQ ID NO:194, SEQ ID NO:195, SEQ ID NO:196, SEQ ID NO:197,SEQ ID NO:198, SEQ ID NO:199, SEQ ID NO:200, SEQ ID NO:201, SEQ IDNO:202, SEQ ID NO:203, SEQ ID NO:204, SEQ ID NO:205, SEQ ID NO:206, SEQID NO:207, SEQ ID NO:208, SEQ ID NO:209, SEQ ID NO:210, SEQ ID NO:211,SEQ ID NO:212, SEQ ID NO:213, SEQ ID NO:214, SEQ ID NO:215, SEQ IDNO:216, SEQ ID NO:217, SEQ ID NO:218, SEQ ID NO:219, SEQ ID NO:220, SEQID NO:221, SEQ ID NO:222, SEQ ID NO:223, and SEQ ID NO:224.
 3. Thepolypeptide as claimed in claim 1, wherein the EF chain is between 6 and12 residues long.
 4. The polypeptide as claimed in claim 1, wherein theEF chain comprises an α-helix.
 5. The polypeptide as claimed in claim 4,wherein the α-helix on the EF chain comprises residues X¹ and X².
 6. Thepolypeptide as claimed in claim 5, wherein β-strands C and D areconnected together by a CD chain, comprising a CD motif selected fromthe group consisting of SEQ ID NO:245, SEQ ID NO:246, SEQ ID NO:247, SEQID NO:248, SEQ ID NO:249, SEQ ID NO:250, SEQ ID NO:251, SEQ ID NO:252,and SEQ ID NO:253, said CD motif beginning at the first or secondresidue of said CD chain.
 7. The polypeptide as claimed in claim 6,wherein the CD motif is SEQ ID NO:251.
 8. The polypeptide as claimed inclaim 6, wherein the CD motif does not form part of an α-helix.
 9. Apolypeptide comprising an antibody constant domain comprising theresidues K and H at positions corresponding to positions 80 and 81 ofSEQ ID NO:6 when said antibody constant domain is aligned with thesequence of SEQ ID NO:6, and characterized in that the antibody constantdomain further comprises a residue selected from the group consisting ofA, G, I, V, L, R, S, T, Q, P, N, M, H, W at a position corresponding toposition 77 of SEQ ID NO:6, pharmaceutically acceptable salts,stereoisomers, tautomers, solvates, and prodrugs thereof.
 10. Apolypeptide as claimed in claim 9, further comprising a residue selectedfrom the group consisting of V, I and L at a position corresponding toresidue 42 of SEQ ID NO:6.
 11. A polypeptide as claimed in claim 9,further comprising a residue selected from the group consisting of D, E,N, and Q at a position corresponding to residue 43 of SEQ ID NO:6.
 12. Apolypeptide as claimed in claim 9, wherein the residues at positionscorresponding to residues 42 and 43 of SEQ ID NO:6 are not in α-helicalformation.
 13. The polypeptide as claimed in claim 1, wherein thepolypeptide is a mammalian antibody constant domain.
 14. The polypeptideas claimed in claim 13, wherein the constant domain is connected to anantibody variable domain.
 15. The polypeptide as claimed in claim 1,wherein the ε-amino group of the side chain of K⁵ of SEQ ID NO:98 iscovalently attached to a linker.
 16. The polypeptide as claimed in claim15, wherein the linker comprises a formula selected from the groupconsisting of X¹—Y—Z¹, X¹-Φ-Y¹—Z¹, and X¹—Y¹-Φ-Z, wherein Φ is acleavable group, X¹ is a group covalently connectable to at least oneEffector Moiety, Y¹ is a linear or branched connecting chain, and Z is agroup covalently connected to the ε-amino group of the side chain of K⁵of SEQ ID NO:98.
 17. The polypeptide as claimed in claim 16, wherein thecleavable group Φ is present, and is of the formula

wherein the wavy line and parallel line each indicate a point ofattachment to either the X¹, Y¹ or Z¹ group as appropriate.
 18. Thepolypeptide as claimed in claim 16, wherein the linker is selected fromthe group consisting of:

wherein m, n, j and k are each independently a range whose lower limitsare selected from the group consisting of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, and 20, and whose upper limit isselected from the group consisting of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,and 30, and wherein the overall length of the linker does not exceed 200atoms.
 19. The polypeptide as claimed in claim 16, wherein the EffectorMoiety is a therapeutic agent, protein, peptide, nucleic acid, aptamer,small molecule, protein agonist, protein antagonist, metabolicregulator, hormone, toxin, growth factor, or diagnostic agent.
 20. Thepolypeptide as claimed in claim 19, wherein the Effector Moiety is atoxin, and comprises the formula:

or a pharmaceutically acceptable salt or solvate thereof, wherein,independently for each occurrence,

R¹¹ is

Y² is —C₂-C₂₀ alkylene-, —C₂-C₂₀ heteroalkylene-; —C₃-C₈ carbocyclo-,-arylene-, —C₃-C₈heterocyclo-, —C₁-C₁₀alkylene-arylene-,-arylene-C₁-C₁₀alkylene-, —C₁-C₁₀alkylene-(C₃-C₈ carbocyclo)-,-(C₃-C₈carbocyclo)-C₁-C₁₀alkylene-, —C₁-C₁₀alkylene-(C₃-C₈heterocyclo)-or —(C₃-C₈ heterocyclo)-C₁-C₁₀alkylene-; Z² is

R¹² is hydrogen, C₁-C₈ alkyl or C₁-C₈ haloalkyl; R^(13A) and R^(13B) areeither of the following: (iii) R^(13A) is hydrogen, C₁-C₈ alkyl, C₁-C₈haloalkyl, C₃-C₈ carbocyclyl, C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl,aralkyl or halogen; and R^(13B) is C₁-C₈ alkyl, C₁-C₈ haloalkyl, C₃-C₈carbocyclyl, C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl or aralkyl orhalogen; or (iv) R^(13A) and R^(13B) taken together are C₂-C₈ alkyleneor C₁-C₈ heteroalkylene; R^(14A) and R^(14B) are either of thefollowing: (iii) R^(14A) is hydrogen, C₁-C₈ alkyl, C₁-C₈ haloalkyl,C₃-C₈ carbocyclyl, C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl or aralkyl;and R^(14B) is hydrogen, C₁-C₈ alkyl, C₁-C₈ haloalkyl, C₃-C₈carbocyclyl, C₁-C₁₀ heterocyclyl, aryl, heteroaralkyl or aralkyl; or(iv) R^(14A) and R^(14B) taken together are C₂-C₈ alkylene or C₁-C₈heteroalkylene; R¹⁵ is

C₁-C₁₀ heterocyclyl, C₃-C₈ carbocycly and C₆-C₁₄ aryl optionallysubstituted with 1, 2, 3, 4 or 5 groups independently selected from thegroup consisting of —C₁-C₈ alkyl, —C₁-C₈ alkyl-N(R′)₂, —C₁-C₈alkyl-C(O)R′, —C₁-C₈ alkyl-C(O)OR′—O—(C₁-C₈ alkyl), —C(O)R′, —OC(O)R′,—C(O)OR′, —C(O)N(R′)₂, —NHC(O)R′, —S(O)₂R′, —S(O)R′, —OH, halogen, —N₃,—N(R′)₂, —CN, —NHC(═NH)NH₂, —NHCONH₂, —S(═O)₂R′ and —SR′, wherein eachR′ is independently selected from the group consisting of hydrogen,C₁-C₈ alkyl and unsubstituted aryl, or two R′ can, together with thenitrogen to which they are attached, form a C₁-C₁₀ heterocyclyl; or R¹⁵is

optionally substituted with 1, 2, 3, 4 or 5 groups independentlyselected from the group consisting of C₁-C₈ alkyl, —C₁-C₈ alkyl-N(R′)₂,—C₁-C₈ alkyl-C(O)R′, —C₁-C₈ alkyl-C(O)OR′, —O—(C₁-C₈ alkyl), —C(O)R,—OC(O)R, —C(O)OR, —C(O)N(R′)₂, —NHC(O)R, —S(O)₂R′, —S(O)R′, —OH,halogen, —N₃, —N(R′)₂, —CN, —NHC(═NH)NH₂, —NHCONH₂, —S(═O)₂R′, —SR′ andarylene-R′, wherein each R′ is independently selected from the groupconsisting of hydrogen, C₁-C₈ alkyl, C₁-C₈heterocyclyl,C₁-C₁₀alkylene-C₃-C₈heterocyclyl and aryl, or two R′ can, together withthe nitrogen to which they are attached, form a C₁-C₁₀ heterocyclyl; R¹⁶is hydrogen, —C₁-C₈ alkyl, —C₂-C₈ alkenyl, —C₂-C₈ alkynyl or —C₁-C₈haloalkyl; R²² is hydrogen, C₁-C₄ alkyl, C₁-C₁₀ heterocyclyl or C₆-C₁₄aryl; R²³ is C₁-C₁₀ heterocyclyl; and R¹⁷ is independently selected foreach occurrence from the group consisting of F, Cl, I and Br; R²⁰ is-aryl, —C₁-C₁₀alkylene-aryl, where aryl on R¹⁰ comprising aryl issubstituted with [R¹⁷]_(h); h is 5; and X is O or S; provided that whenR^(13A) is hydrogen X is S.
 21. The polypeptide as claimed in claim 19,wherein the Effector Moiety is a toxin, and is selected from the groupconsisting of


22. The polypeptide as claimed in claim 1, wherein the polypeptidecomprises an antibody constant light (CL) domain.
 23. The polypeptide asclaimed in claim 22, wherein the CL domain is a kappa domain (CLκ). 24.The polypeptide as claimed in claim 23, wherein the CLκ comprises asequence selected from the group consisting of SEQ ID NO:37, SEQ IDNO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ IDNO:44, SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:50, SEQ IDNO:51, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:104, SEQ ID NO:105, SEQ IDNO:106, SEQ ID NO:119, SEQ ID NO:120, SEQ ID NO:121, and SEQ ID NO:122.25. The polypeptide as claimed in claim 23, wherein the CLκ comprises anN-terminal portion defined by SEQ ID NO:225 and a C′ terminal portiondefined by SEQ ID NO:226 contiguously connected together by anintermediate sequence selected from the group consisting of SEQ IDNO:99, SEQ ID NO:100, SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:103, SEQID NO:115, SEQ ID NO:116, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:123,SEQ ID NO:124, SEQ ID NO:125, SEQ ID NO:126, SEQ ID NO:170, SEQ IDNO:171, SEQ ID NO:172, SEQ ID NO:173, SEQ ID NO:174, SEQ ID NO:175, SEQID NO:176, SEQ ID NO:177, SEQ ID NO:178, SEQ ID NO:179, SEQ ID NO:180,SEQ ID NO:181, SEQ ID NO:182, SEQ ID NO:183, SEQ ID NO:184, SEQ IDNO:185, SEQ ID NO:186, SEQ ID NO:187, SEQ ID NO:188, SEQ ID NO:189, SEQID NO:190, SEQ ID NO:191, SEQ ID NO:192, SEQ ID NO:193, SEQ ID NO:194,SEQ ID NO:195, SEQ ID NO:196, SEQ ID NO:197, SEQ ID NO:198, SEQ IDNO:199, SEQ ID NO:200, SEQ ID NO:201, SEQ ID NO:202, SEQ ID NO:203, SEQID NO:204, SEQ ID NO:205, SEQ ID NO:206, SEQ ID NO:207, SEQ ID NO:208,SEQ ID NO:209, SEQ ID NO:210, SEQ ID NO:211, SEQ ID NO:212, SEQ IDNO:213, SEQ ID NO:214, SEQ ID NO:215, SEQ ID NO:216, SEQ ID NO:217, SEQID NO:218, SEQ ID NO:219, SEQ ID NO:220, SEQ ID NO:221, SEQ ID NO:222,SEQ ID NO:223, and SEQ ID NO:224.
 26. The polypeptide as claimed inclaim 22, wherein the CL domain is a lambda domain (CLλ), and comprisesa sequence selected from the group consisting of SEQ ID NO:60, SEQ IDNO:61, SEQ ID NO:141, SEQ ID NO:144, SEQ ID NO:143, SEQ ID NO:236, SEQID NO:237, SEQ ID NO:238, SEQ ID NO:239, SEQ ID NO:240, SEQ ID NO:241,SEQ ID NO:242, SEQ ID NO:243, and SEQ ID NO:244.
 27. The polypeptide asclaimed in claim 22, wherein the CL domain is a lambda domain (CLλ), andwherein the CLλ comprises an N′ terminal portion defined by one of SEQID NO:227, SEQ ID NO:228, SEQ ID NO:229, SEQ ID NO:230, SEQ ID NO:231,SEQ ID NO:232, or SEQ ID NO:233 contiguously connected together by anintermediate sequence to a C′ terminal portion defined by either of SEQID NO:234 or SEQ ID NO:235, the intermediate sequence being selectedfrom the group consisting of SEQ ID NO:99, SEQ ID NO:100, SEQ ID NO:101,SEQ ID NO:102, SEQ ID NO:103, SEQ ID NO:115, SEQ ID NO:116, SEQ IDNO:117, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:124, SEQ ID NO:125, SEQID NO:126, SEQ ID NO:170, SEQ ID NO:171, SEQ ID NO:172, SEQ ID NO:173,SEQ ID NO:174, SEQ ID NO:175, SEQ ID NO:176, SEQ ID NO:177, SEQ IDNO:178, SEQ ID NO:179, SEQ ID NO:180, SEQ ID NO:181, SEQ ID NO:182, SEQID NO:183, SEQ ID NO:184, SEQ ID NO:185, SEQ ID NO:186, SEQ ID NO:187,SEQ ID NO:188, SEQ ID NO:189, SEQ ID NO:190, SEQ ID NO:191, SEQ IDNO:192, SEQ ID NO:193, SEQ ID NO:194, SEQ ID NO:195, SEQ ID NO:196, SEQID NO:197, SEQ ID NO:198, SEQ ID NO:199, SEQ ID NO:200, SEQ ID NO:201,SEQ ID NO:202, SEQ ID NO:203, SEQ ID NO:204, SEQ ID NO:205, SEQ IDNO:206, SEQ ID NO:207, SEQ ID NO:208, SEQ ID NO:209, SEQ ID NO:210, SEQID NO:211, SEQ ID NO:212, SEQ ID NO:213, SEQ ID NO:214, SEQ ID NO:215,SEQ ID NO:216, SEQ ID NO:217, SEQ ID NO:218, SEQ ID NO:219, SEQ IDNO:220, SEQ ID NO:221, SEQ ID NO:222, SEQ ID NO:223, and SEQ ID NO:224.28. The polypeptide as claimed in claim 1, comprising a sequenceselected from the group consisting of SEQ ID NO:37, SEQ ID NO:38, SEQ IDNO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:44, SEQ IDNO:46, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ IDNO:52, SEQ ID NO:54, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:77, SEQ IDNO:78, SEQ ID NO:94, SEQ ID NO:95, SEQ ID NO:96, SEQ ID NO:97, SEQ IDNO:104, SEQ ID NO:105, SEQ ID NO:106, SEQ ID NO:119, SEQ ID NO:120, SEQID NO:121, SEQ ID NO:122, SEQ ID NO:127, SEQ ID NO:128, SEQ ID NO:129,SEQ ID NO:134, SEQ ID NO:135, SEQ ID NO:140, SEQ ID NO:141, SEQ IDNO:142, SEQ ID NO:143, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:149, SEQID NO:150, SEQ ID NO:151, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:159,SEQ ID NO:160, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NO:165, SEQ IDNO:167, SEQ ID NO:168, SEQ ID NO:169, SEQ ID NO:236, SEQ ID NO:237, SEQID NO:238, SEQ ID NO:239, SEQ ID NO:240, SEQ ID NO:241, and SEQ IDNO:254, or a polypeptide at least about 85% identical thereof.
 29. Acomposition comprising the polypeptide as claimed in claim 15, whereinat least about 70% of the Linker in the composition or sample isconjugated to the ε-amino group of the side chain of K⁵ of SEQ ID NO:98.30. A composition comprising multiples of the polypeptide as claimed inclaim 15, wherein at least about 70% of the polypeptides comprises theLinker covalently attached to the ε-amino group of the side chain of K⁵of SEQ ID NO:98.
 31. An antibody, or antigen binding portion thereof,wherein the antibody comprises the polypeptide as claimed in claim 1.32. The antibody as claimed in claim 31, wherein the antibody comprisesVH and VL domains from an antibody selected from the group consisting ofh38C2, rituximab, cetuximab, infliximab, adalimumab, natalizumab,omalizumab, ranibizumab, trastuzumab and palivizumab.
 33. Apharmaceutical composition comprising the polypeptide as claimed inclaim 1, and further comprising an acceptable carrier.
 34. A nucleicacid encoding the polypeptide as claimed in claim
 1. 35. A host cellcomprising the nucleic acid as claimed in claim
 34. 36. A vectorcomprising the nucleic acid as claimed in claim
 35. 37. A method forpreparing a multifunctional antibody conjugate (MAC) comprising apolypeptide as claimed in claim 1, comprising covalently attaching theLinker to a leaving group Z* of the formula:

where R¹ is F or Cl, h=2, 3, 4 or 5 and reacting the Linker-Z* groupwith the polypeptide.